cardinal_classification: classification.xml annotate

author	galaxyp
date	Mon, 01 Oct 2018 00:59:14 -0400
parents
children	33579f05d1f8

rev	line source
0 7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1 <tool id="cardinal_classification" name="MSI classification" version="@VERSION@.0">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	2 <description>spatial classification of mass spectrometry imaging data</description>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	3 <macros>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	4 <import>macros.xml</import>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	5 </macros>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	6 <expand macro="requirements">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	7 <requirement type="package" version="2.2.1">r-gridextra</requirement>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	8 <requirement type="package" version="0.20-35">r-lattice</requirement>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	9 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	10 </expand>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	11 <command detect_errors="exit_code">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	12 <![CDATA[
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	13
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	14 @INPUT_LINKING@
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	15 cat '${MSI_segmentation}' &&
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	16 Rscript '${MSI_segmentation}'
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	17
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	18 ]]>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	19 </command>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	20 <configfiles>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	21 <configfile name="MSI_segmentation"><![CDATA[
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	22
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	23
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	24 ################################# load libraries and read file #########################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	25
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	26 library(Cardinal)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	27 library(gridExtra)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	28 library(lattice)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	29 library(ggplot2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	30
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	31 @READING_MSIDATA@
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	32
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	33 ## create full matrix to make processed imzML files compatible with classification
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	34 iData(msidata) <- iData(msidata)[]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	35
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	36 @DATA_PROPERTIES@
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	37
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	38 ######################################## PDF ###################################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	39 ################################################################################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	40 ################################################################################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	41
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	42 Title = "Prediction"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	43
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	44 #if str( $type_cond.type_method) == "training":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	45
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	46 Title = "$type_cond.method_cond.class_method"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	47 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	48
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	49 pdf("classificationpdf.pdf", fonts = "Times", pointsize = 12)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	50 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	51
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	52
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	53 title(main=paste0(Title," for file: \n\n", "$infile.display_name"))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	54
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	55
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	56 ##################### I) numbers and control plots #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	57 ###############################################################################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	58
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	59 ## table with values
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	60 grid.table(property_df, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	61
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	62
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	63 if (npeaks > 0 && sum(is.na(spectra(msidata)))==0){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	64
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	65 opar <- par()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	66
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	67 ######################## II) Training #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	68 #############################################################################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	69 #if str( $type_cond.type_method) == "training":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	70 print("training")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	71
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	72
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	73 ## load y response (will be needed in every training scenario)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	74
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	75 y_tabular = read.delim("$type_cond.annotation_file", header = $type_cond.tabular_header, stringsAsFactors = FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	76
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	77 #if str($type_cond.column_fold) == "None":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	78 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response)]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	79 #else
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	80 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response, $type_cond.column_fold)]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	81 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	82
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	83 colnames(y_input)[1:2] = c("x", "y")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	84 ## merge with coordinate information of msidata
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	85 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	86 colnames(msidata_coordinates)[3] = "pixel_index"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	87 merged_response = merge(msidata_coordinates, y_input, by=c("x", "y"), all.x=TRUE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	88 merged_response[is.na(merged_response)] = "NA"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	89 merged_response = merged_response[order(merged_response\$pixel_index),]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	90 y_vector = as.factor(merged_response[,4])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	91
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	92 ## plot of y vector
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	93
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	94 position_df = cbind(coord(msidata)[,1:2], y_vector)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	95 y_plot = ggplot(position_df, aes(x=x, y=y, fill=y_vector))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	96 geom_tile() +
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	97 coord_fixed()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	98 ggtitle("Distribution of the response variable y")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	99 theme_bw()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	100 theme(text=element_text(family="ArialMT", face="bold", size=15))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	101 theme(legend.position="bottom",legend.direction="vertical")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	102 guides(fill=guide_legend(ncol=4,byrow=TRUE))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	103 coord_labels = aggregate(cbind(x,y)~y_vector, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	104 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$y_vector)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	105 print(y_plot)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	106
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	107
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	108 ## plot of folds
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	109
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	110 #if str($type_cond.column_fold) != "None":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	111 fold_vector = as.factor(merged_response[,5])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	112
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	113
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	114 position_df = cbind(coord(msidata)[,1:2], fold_vector)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	115 fold_plot = ggplot(position_df, aes(x=x, y=y, fill=fold_vector))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	116 geom_tile() +
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	117 coord_fixed()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	118 ggtitle("Distribution of the fold variable")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	119 theme_bw()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	120 theme(text=element_text(family="ArialMT", face="bold", size=15))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	121 theme(legend.position="bottom",legend.direction="vertical")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	122 guides(fill=guide_legend(ncol=4,byrow=TRUE))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	123 coord_labels = aggregate(cbind(x,y)~fold_vector, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	124 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$fold_vector)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	125 print(fold_plot)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	126
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	127 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	128
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	129 ######################## PLS #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	130 #if str( $type_cond.method_cond.class_method) == "PLS":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	131 print("PLS")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	132
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	133 ######################## PLS - CV #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	134 #if str( $type_cond.method_cond.analysis_cond.PLS_method) == "cvapply":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	135 print("PLS cv")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	136
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	137 ## set variables for components and number of response groups
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	138 components = c($type_cond.method_cond.analysis_cond.plscv_comp)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	139 number_groups = length(levels(y_vector))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	140
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	141 ## PLS-cvApply:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	142 msidata.cv.pls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "PLS", ncomp = components)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	143
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	144 ## create table with summary
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	145 count = 1
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	146 summary_plscv = list()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	147 accuracy_vector = numeric()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	148 for (iteration in components){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	149 summary_iteration = summary(msidata.cv.pls)\$accuracy[[paste0("ncomp = ", iteration)]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	150 ## change class of numbers into numeric to round and calculate mean
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	151 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	152 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	153 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	154 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	155 summary_iteration4 = t(summary_iteration3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	156 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	157 summary_plscv[[count]] = summary_iteration5
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	158 count = count+1} ## create list with summary table for each component
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	159 summary_plscv = do.call(rbind, summary_plscv)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	160 summary_df = as.data.frame(summary_plscv)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	161 colnames(summary_df) = NULL
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	162
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	163 ## plots
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	164 ## plot to find ncomp with highest accuracy
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	165 plot(components, accuracy_vector, ylab = "mean accuracy",type="o", main="Mean accuracy of PLS classification")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	166 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	167 ## one image for each sample/fold, 4 images per page
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	168 minimumy = min(coord(msidata.cv.pls)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	169 maximumy = max(coord(msidata.cv.pls)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	170 image(msidata.cv.pls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy),layout = c(2, 2))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	171
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	172 ## print table with summary in pdf
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	173 par(opar)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	174 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	175 title(main="Summary for the different components\n", adj=0.5)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	176 ## 20 rows fits in one page:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	177 if (nrow(summary_df)<=20){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	178 grid.table(summary_df, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	179 }else{
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	180 grid.table(summary_df[1:20,], rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	181 mincount = 21
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	182 maxcount = 40
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	183 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	184 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	185 if (maxcount <= nrow(summary_df)){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	186 grid.table(summary_df[mincount:maxcount,], rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	187 mincount = mincount+20
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	188 maxcount = maxcount+20
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	189 }else{### stop last page with last sample otherwise NA in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	190 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	191 }
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	192 }
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	193
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	194 ## optional output as .RData
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	195 #if $output_rdata:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	196 save(msidata.cv.pls, file="$classification_rdata")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	197 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	198
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	199
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	200 ######################## PLS - analysis ###########################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	201 #elif str( $type_cond.method_cond.analysis_cond.PLS_method) == "PLS_analysis":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	202 print("PLS analysis")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	203
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	204 ## set variables for components and number of response groups
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	205 component = c($type_cond.method_cond.analysis_cond.pls_comp)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	206 number_groups = length(levels(y_vector))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	207
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	208 ### pls analysis and coefficients plot
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	209 msidata.pls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.analysis_cond.pls_scale)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	210 plot(msidata.pls, main="PLS coefficients per m/z")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	211
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	212 ### summary table of PLS
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	213 summary_table = summary(msidata.pls)\$accuracy[[paste0("ncomp = ",component)]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	214 summary_table2 = round(as.numeric(summary_table), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	215 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	216 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	217 summary_table4 = t(summary_table3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	218 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	219 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	220 grid.table(summary_table5, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	221
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	222 ### image of the best m/z
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	223 minimumy = min(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	224 maximumy = max(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	225 print(image(msidata, mz = topLabels(msidata.pls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy), smooth.image="gaussian", main="best m/z heatmap"))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	226
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	227 ### m/z and pixel information output
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	228 pls_classes = data.frame(msidata.pls\$classes[[1]])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	229 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	230 pixel_names = gsub(" = ", "y_", pixel_names)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	231 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	232 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	233
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	234 pls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, pls_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	235 colnames(pls_classes2) = c("pixel names", "x", "y","predicted condition")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	236 pls_toplabels = topLabels(msidata.pls, n=$type_cond.method_cond.analysis_cond.pls_toplabels)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	237 write.table(pls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	238 write.table(pls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	239
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	240 ## image with predicted classes
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	241 prediction_df = cbind(coord(msidata.pls)[,1:2], pls_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	242 colnames(prediction_df) = c("x", "y", "predicted_classes")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	243
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	244 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	245 geom_tile() +
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	246 coord_fixed()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	247 ggtitle("Predicted condition for each pixel")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	248 theme_bw()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	249 theme(text=element_text(family="ArialMT", face="bold", size=15))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	250 theme(legend.position="bottom",legend.direction="vertical")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	251 guides(fill=guide_legend(ncol=4,byrow=TRUE))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	252 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	253 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	254 print(prediction_plot)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	255
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	256 ### optional output as .RData
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	257 #if $output_rdata:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	258 save(msidata.pls, file="$classification_rdata")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	259 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	260
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	261 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	262
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	263 ######################## OPLS #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	264 #elif str( $type_cond.method_cond.class_method) == "OPLS":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	265 print("OPLS")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	266
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	267 ######################## OPLS -CV #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	268 #if str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_cvapply":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	269 print("OPLS cv")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	270
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	271 ## set variables for components and number of response groups
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	272 components = c($type_cond.method_cond.opls_analysis_cond.opls_cvcomp)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	273 number_groups = length(levels(y_vector))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	274
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	275 ## OPLS-cvApply:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	276 msidata.cv.opls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "OPLS", ncomp = components, keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew_cv)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	277
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	278 ## create table with summary
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	279 count = 1
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	280 summary_oplscv = list()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	281 accuracy_vector = numeric()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	282 for (iteration in components){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	283
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	284 summary_iteration = summary(msidata.cv.opls)\$accuracy[[paste0("ncomp = ", iteration)]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	285 ## change class of numbers into numeric to round and calculate mean
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	286 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	287 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	288 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	289 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	290 summary_iteration4 = t(summary_iteration3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	291 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	292 summary_oplscv[[count]] = summary_iteration5
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	293 count = count+1} ## create list with summary table for each component
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	294 summary_oplscv = do.call(rbind, summary_oplscv)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	295 summary_df = as.data.frame(summary_oplscv)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	296 colnames(summary_df) = NULL
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	297
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	298 ## plots
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	299 ## plot to find ncomp with highest accuracy
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	300 plot(components, accuracy_vector, ylab = "mean accuracy", type="o", main="Mean accuracy of OPLS classification")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	301 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	302 ## one image for each sample/fold, 4 images per page
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	303 minimumy = min(coord(msidata.cv.opls)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	304 maximumy = max(coord(msidata.cv.opls)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	305 image(msidata.cv.opls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy),layout = c(2, 2))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	306
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	307 ## print table with summary in pdf
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	308 par(opar)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	309 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	310 title(main="Summary for the different components\n", adj=0.5)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	311 ## 20 rows fits in one page:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	312 if (nrow(summary_df)<=20){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	313 grid.table(summary_df, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	314 }else{
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	315 grid.table(summary_df[1:20,], rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	316 mincount = 21
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	317 maxcount = 40
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	318 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	319 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	320 if (maxcount <= nrow(summary_df)){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	321 grid.table(summary_df[mincount:maxcount,], rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	322 mincount = mincount+20
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	323 maxcount = maxcount+20
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	324 }else{### stop last page with last sample otherwise NA in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	325 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	326 }
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	327 }
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	328
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	329 ## optional output as .RData
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	330 #if $output_rdata:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	331 save(msidata.cv.opls, file="$classification_rdata")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	332 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	333
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	334
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	335 ######################## OPLS -analysis ###########################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	336 #elif str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_analysis":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	337 print("OPLS analysis")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	338
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	339 ## set variables for components and number of response groups
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	340 component = c($type_cond.method_cond.opls_analysis_cond.opls_comp)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	341 number_groups = length(levels(y_vector))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	342
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	343
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	344 ### opls analysis and coefficients plot
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	345 msidata.opls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.opls_analysis_cond.opls_scale, keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	346 plot(msidata.opls, main="OPLS coefficients per m/z")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	347
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	348 ### summary table of OPLS
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	349 summary_table = summary(msidata.opls)\$accuracy[[paste0("ncomp = ",component)]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	350 summary_table2 = round(as.numeric(summary_table), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	351 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	352 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	353 summary_table4 = t(summary_table3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	354 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	355 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	356 grid.table(summary_table5, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	357
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	358 ### image of the best m/z
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	359 minimumy = min(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	360 maximumy = max(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	361 print(image(msidata, mz = topLabels(msidata.opls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy), main="best m/z heatmap"))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	362
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	363 ## m/z and pixel information output
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	364 opls_classes = data.frame(msidata.opls\$classes[[1]])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	365 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	366 pixel_names = gsub(" = ", "y_", pixel_names)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	367 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	368 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	369 opls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, opls_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	370 colnames(opls_classes2) = c("pixel names", "x", "y","predicted condition")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	371
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	372 opls_toplabels = topLabels(msidata.opls, n=$type_cond.method_cond.opls_analysis_cond.opls_toplabels)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	373 write.table(opls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	374 write.table(opls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	375
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	376 ## image with predicted classes
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	377 prediction_df = cbind(coord(msidata.opls)[,1:2], opls_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	378 colnames(prediction_df) = c("x", "y", "predicted_classes")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	379
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	380 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	381 geom_tile() +
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	382 coord_fixed()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	383 ggtitle("Predicted condition for each pixel")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	384 theme_bw()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	385 theme(text=element_text(family="ArialMT", face="bold", size=15))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	386 theme(legend.position="bottom",legend.direction="vertical")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	387 guides(fill=guide_legend(ncol=4,byrow=TRUE))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	388 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	389 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	390 print(prediction_plot)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	391
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	392 ## optional output as .RData
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	393 #if $output_rdata:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	394 save(msidata.opls, file="$classification_rdata")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	395 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	396 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	397
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	398
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	399 ######################## SSC #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	400 #elif str( $type_cond.method_cond.class_method) == "spatialShrunkenCentroids":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	401 print("SSC")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	402
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	403 ######################## SSC - CV #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	404 #if str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_cvapply":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	405 print("SSC cv")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	406
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	407 ## set variables for components and number of response groups
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	408 number_groups = length(levels(y_vector))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	409
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	410 ## SSC-cvApply:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	411 msidata.cv.ssc <- cvApply(msidata, .y = y_vector,.fold = fold_vector,.fun = "spatialShrunkenCentroids", r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	412
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	413 ## create table with summary
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	414 count = 1
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	415 summary_ssccv = list()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	416 accuracy_vector = numeric()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	417 iteration_vector = character()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	418 for (iteration in names(msidata.cv.ssc@resultData[[1]][,1])){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	419
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	420 summary_iteration = summary(msidata.cv.ssc)\$accuracy[[iteration]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	421 ## change class of numbers into numeric to round and calculate mean
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	422 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	423 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	424 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	425 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	426 summary_iteration4 = t(summary_iteration3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	427 summary_iteration5 = cbind(c(iteration, colnames(summary_iteration)), summary_iteration4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	428 summary_ssccv[[count]] = summary_iteration5
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	429 iteration_vector[count] = unlist(strsplit(iteration, "[,]"))[3]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	430 count = count+1} ## create list with summary table for each component
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	431 summary_ssccv = do.call(rbind, summary_ssccv)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	432 summary_df = as.data.frame(summary_ssccv)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	433 colnames(summary_df) = NULL
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	434
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	435 ## plot to find parameters with highest accuracy
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	436 plot(c($type_cond.method_cond.ssc_s),accuracy_vector[!duplicated(iteration_vector)], type="o",ylab="Mean accuracy", xlab = "Shrinkage parameter (s)", main="Mean accuracy of SSC classification")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	437 best_params = names(msidata.cv.ssc@resultData[[1]][,1])[which.max(accuracy_vector)] ## find parameters with max. accuracy
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	438 r_value = as.numeric(substring(unlist(strsplit(best_params, ","))[1], 4))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	439 s_value = as.numeric(substring(unlist(strsplit(best_params, ","))[3], 5)) ## remove space
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	440 minimumy = min(coord(msidata.cv.ssc)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	441 maximumy = max(coord(msidata.cv.ssc)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	442 image(msidata.cv.ssc, model = list( r = r_value, s = s_value ), ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy),layout=c(2,2))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	443
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	444 ## print table with summary in pdf
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	445 par(opar)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	446 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	447 title(main="Summary for the different parameters\n", adj=0.5)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	448 ## 20 rows fits in one page:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	449 if (nrow(summary_df)<=20){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	450 grid.table(summary_df, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	451 }else{
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	452 grid.table(summary_df[1:20,], rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	453 mincount = 21
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	454 maxcount = 40
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	455 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	456 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	457 if (maxcount <= nrow(summary_df)){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	458 grid.table(summary_df[mincount:maxcount,], rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	459 mincount = mincount+20
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	460 maxcount = maxcount+20
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	461 }else{### stop last page with last sample otherwise NA in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	462 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	463 }
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	464 }
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	465
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	466 ## optional output as .RData
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	467 #if $output_rdata:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	468 save(msidata.cv.ssc, file="$classification_rdata")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	469 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	470
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	471 ######################## SSC -analysis ###########################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	472 #elif str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_analysis":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	473 print("SSC analysis")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	474
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	475 ## set variables for components and number of response groups
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	476 number_groups = length(levels(y_vector))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	477
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	478 ## SSC analysis and plot
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	479 msidata.ssc <- spatialShrunkenCentroids(msidata, y = y_vector, .fold = fold_vector,
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	480 r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	481 plot(msidata.ssc, mode = "tstatistics", model = list("r" = c($type_cond.method_cond.ssc_r), "s" = c($type_cond.method_cond.ssc_s)))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	482
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	483 ### summary table SSC
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	484 ##############summary_table = summary(msidata.ssc)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	485 summary_table = summary(msidata.ssc)\$accuracy[[names(msidata.ssc@resultData)]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	486 summary_table2 = round(as.numeric(summary_table), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	487 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	488 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	489 summary_table4 = t(summary_table3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	490 summary_table5 = cbind(c(names(msidata.ssc@resultData),colnames(summary_table)), summary_table4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	491 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	492 grid.table(summary_table5, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	493
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	494 ### image of the best m/z
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	495 minimumy = min(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	496 maximumy = max(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	497 print(image(msidata, mz = topLabels(msidata.ssc)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy), main="best m/z heatmap"))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	498
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	499 ## m/z and pixel information output
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	500 ssc_classes = data.frame(msidata.ssc\$classes[[1]])

0

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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1 <tool id="cardinal_classification" name="MSI classification" version="@VERSION@.0">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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2 <description>spatial classification of mass spectrometry imaging data</description>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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3 <macros>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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4 <import>macros.xml</import>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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5 </macros>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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6 <expand macro="requirements">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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7 <requirement type="package" version="2.2.1">r-gridextra</requirement>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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8 <requirement type="package" version="0.20-35">r-lattice</requirement>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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9 <requirement type="package" version="2.2.1">r-ggplot2</requirement>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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10 </expand>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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11 <command detect_errors="exit_code">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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12 <![CDATA[

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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13

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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14 @INPUT_LINKING@

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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15 cat '${MSI_segmentation}' &&

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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16 Rscript '${MSI_segmentation}'

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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17

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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18 ]]>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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19 </command>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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20 <configfiles>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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21 <configfile name="MSI_segmentation"><![CDATA[

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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22

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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23

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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24 ################################# load libraries and read file #########################

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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25

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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26 library(Cardinal)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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27 library(gridExtra)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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28 library(lattice)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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29 library(ggplot2)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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30

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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31 @READING_MSIDATA@

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32

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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33 ## create full matrix to make processed imzML files compatible with classification

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34 iData(msidata) <- iData(msidata)[]

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35

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36 @DATA_PROPERTIES@

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37

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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38 ######################################## PDF ###################################

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39 ################################################################################

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40 ################################################################################

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41

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42 Title = "Prediction"

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43

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44 #if str( $type_cond.type_method) == "training":

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45

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46 Title = "$type_cond.method_cond.class_method"

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47 #end if

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48

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49 pdf("classificationpdf.pdf", fonts = "Times", pointsize = 12)

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50 plot(0,type='n',axes=FALSE,ann=FALSE)

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51

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52

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53 title(main=paste0(Title," for file: \n\n", "$infile.display_name"))

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54

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55

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56 ##################### I) numbers and control plots #############################

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57 ###############################################################################

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58

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59 ## table with values

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60 grid.table(property_df, rows= NULL)

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61

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62

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63 if (npeaks > 0 && sum(is.na(spectra(msidata)))==0){

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64

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65 opar <- par()

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66

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67 ######################## II) Training #############################

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68 #############################################################################

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69 #if str( $type_cond.type_method) == "training":

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70 print("training")

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71

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72

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73 ## load y response (will be needed in every training scenario)

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74

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75 y_tabular = read.delim("$type_cond.annotation_file", header = $type_cond.tabular_header, stringsAsFactors = FALSE)

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76

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77 #if str($type_cond.column_fold) == "None":

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78 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response)]

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79 #else

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80 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response, $type_cond.column_fold)]

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81 #end if

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82

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83 colnames(y_input)[1:2] = c("x", "y")

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84 ## merge with coordinate information of msidata

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85 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))

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86 colnames(msidata_coordinates)[3] = "pixel_index"

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87 merged_response = merge(msidata_coordinates, y_input, by=c("x", "y"), all.x=TRUE)

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88 merged_response[is.na(merged_response)] = "NA"

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89 merged_response = merged_response[order(merged_response\$pixel_index),]

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90 y_vector = as.factor(merged_response[,4])

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91

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92 ## plot of y vector

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93

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94 position_df = cbind(coord(msidata)[,1:2], y_vector)

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95 y_plot = ggplot(position_df, aes(x=x, y=y, fill=y_vector))+

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96 geom_tile() +

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97 coord_fixed()+

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98 ggtitle("Distribution of the response variable y")+

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99 theme_bw()+

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100 theme(text=element_text(family="ArialMT", face="bold", size=15))+

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101 theme(legend.position="bottom",legend.direction="vertical")+

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102 guides(fill=guide_legend(ncol=4,byrow=TRUE))

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103 coord_labels = aggregate(cbind(x,y)~y_vector, data=position_df, mean, na.rm=TRUE, na.action="na.pass")

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104 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$y_vector)

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105 print(y_plot)

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106

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107

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108 ## plot of folds

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109

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110 #if str($type_cond.column_fold) != "None":

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111 fold_vector = as.factor(merged_response[,5])

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112

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113

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114 position_df = cbind(coord(msidata)[,1:2], fold_vector)

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115 fold_plot = ggplot(position_df, aes(x=x, y=y, fill=fold_vector))+

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116 geom_tile() +

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117 coord_fixed()+

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118 ggtitle("Distribution of the fold variable")+

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119 theme_bw()+

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120 theme(text=element_text(family="ArialMT", face="bold", size=15))+

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121 theme(legend.position="bottom",legend.direction="vertical")+

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122 guides(fill=guide_legend(ncol=4,byrow=TRUE))

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123 coord_labels = aggregate(cbind(x,y)~fold_vector, data=position_df, mean, na.rm=TRUE, na.action="na.pass")

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124 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$fold_vector)

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125 print(fold_plot)

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126

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127 #end if

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128

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129 ######################## PLS #############################

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130 #if str( $type_cond.method_cond.class_method) == "PLS":

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131 print("PLS")

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132

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133 ######################## PLS - CV #############################

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134 #if str( $type_cond.method_cond.analysis_cond.PLS_method) == "cvapply":

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135 print("PLS cv")

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136

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137 ## set variables for components and number of response groups

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138 components = c($type_cond.method_cond.analysis_cond.plscv_comp)

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139 number_groups = length(levels(y_vector))

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140

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141 ## PLS-cvApply:

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142 msidata.cv.pls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "PLS", ncomp = components)

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143

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144 ## create table with summary

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145 count = 1

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146 summary_plscv = list()

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147 accuracy_vector = numeric()

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148 for (iteration in components){

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149 summary_iteration = summary(msidata.cv.pls)\$accuracy[[paste0("ncomp = ", iteration)]]

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150 ## change class of numbers into numeric to round and calculate mean

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151 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)

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152 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)

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153 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot

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154 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table

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155 summary_iteration4 = t(summary_iteration3)

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156 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)

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157 summary_plscv[[count]] = summary_iteration5

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158 count = count+1} ## create list with summary table for each component

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159 summary_plscv = do.call(rbind, summary_plscv)

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160 summary_df = as.data.frame(summary_plscv)

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161 colnames(summary_df) = NULL

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162

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163 ## plots

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164 ## plot to find ncomp with highest accuracy

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165 plot(components, accuracy_vector, ylab = "mean accuracy",type="o", main="Mean accuracy of PLS classification")

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166 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy

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167 ## one image for each sample/fold, 4 images per page

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168 minimumy = min(coord(msidata.cv.pls)[,2])

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169 maximumy = max(coord(msidata.cv.pls)[,2])

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170 image(msidata.cv.pls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),layout = c(2, 2))

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171

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172 ## print table with summary in pdf

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173 par(opar)

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174 plot(0,type='n',axes=FALSE,ann=FALSE)

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175 title(main="Summary for the different components\n", adj=0.5)

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176 ## 20 rows fits in one page:

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177 if (nrow(summary_df)<=20){

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178 grid.table(summary_df, rows= NULL)

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179 }else{

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180 grid.table(summary_df[1:20,], rows= NULL)

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181 mincount = 21

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182 maxcount = 40

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183 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){

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184 plot(0,type='n',axes=FALSE,ann=FALSE)

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185 if (maxcount <= nrow(summary_df)){

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186 grid.table(summary_df[mincount:maxcount,], rows= NULL)

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187 mincount = mincount+20

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188 maxcount = maxcount+20

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189 }else{### stop last page with last sample otherwise NA in table

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190 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}

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191 }

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192 }

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193

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194 ## optional output as .RData

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195 #if $output_rdata:

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196 save(msidata.cv.pls, file="$classification_rdata")

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197 #end if

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198

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199

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200 ######################## PLS - analysis ###########################

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201 #elif str( $type_cond.method_cond.analysis_cond.PLS_method) == "PLS_analysis":

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202 print("PLS analysis")

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203

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204 ## set variables for components and number of response groups

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205 component = c($type_cond.method_cond.analysis_cond.pls_comp)

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206 number_groups = length(levels(y_vector))

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207

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208 ### pls analysis and coefficients plot

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209 msidata.pls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.analysis_cond.pls_scale)

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210 plot(msidata.pls, main="PLS coefficients per m/z")

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211

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212 ### summary table of PLS

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213 summary_table = summary(msidata.pls)\$accuracy[[paste0("ncomp = ",component)]]

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214 summary_table2 = round(as.numeric(summary_table), digits=2)

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215 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)

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216 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table

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217 summary_table4 = t(summary_table3)

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218 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)

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219 plot(0,type='n',axes=FALSE,ann=FALSE)

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220 grid.table(summary_table5, rows= NULL)

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221

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222 ### image of the best m/z

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223 minimumy = min(coord(msidata)[,2])

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224 maximumy = max(coord(msidata)[,2])

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225 print(image(msidata, mz = topLabels(msidata.pls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), smooth.image="gaussian", main="best m/z heatmap"))

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226

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227 ### m/z and pixel information output

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228 pls_classes = data.frame(msidata.pls\$classes[[1]])

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229 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))

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230 pixel_names = gsub(" = ", "y_", pixel_names)

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231 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]

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232 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]

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233

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234 pls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, pls_classes)

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235 colnames(pls_classes2) = c("pixel names", "x", "y","predicted condition")

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236 pls_toplabels = topLabels(msidata.pls, n=$type_cond.method_cond.analysis_cond.pls_toplabels)

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237 write.table(pls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")

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238 write.table(pls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")

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239

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240 ## image with predicted classes

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241 prediction_df = cbind(coord(msidata.pls)[,1:2], pls_classes)

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242 colnames(prediction_df) = c("x", "y", "predicted_classes")

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243

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244 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+

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245 geom_tile() +

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246 coord_fixed()+

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247 ggtitle("Predicted condition for each pixel")+

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248 theme_bw()+

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249 theme(text=element_text(family="ArialMT", face="bold", size=15))+

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250 theme(legend.position="bottom",legend.direction="vertical")+

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251 guides(fill=guide_legend(ncol=4,byrow=TRUE))

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252 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")

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253 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)

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254 print(prediction_plot)

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255

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256 ### optional output as .RData

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257 #if $output_rdata:

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258 save(msidata.pls, file="$classification_rdata")

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259 #end if

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260

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261 #end if

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262

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263 ######################## OPLS #############################

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264 #elif str( $type_cond.method_cond.class_method) == "OPLS":

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265 print("OPLS")

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266

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267 ######################## OPLS -CV #############################

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268 #if str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_cvapply":

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269 print("OPLS cv")

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270

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271 ## set variables for components and number of response groups

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272 components = c($type_cond.method_cond.opls_analysis_cond.opls_cvcomp)

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273 number_groups = length(levels(y_vector))

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274

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275 ## OPLS-cvApply:

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276 msidata.cv.opls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "OPLS", ncomp = components, keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew_cv)

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277

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278 ## create table with summary

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279 count = 1

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280 summary_oplscv = list()

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281 accuracy_vector = numeric()

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282 for (iteration in components){

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283

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284 summary_iteration = summary(msidata.cv.opls)\$accuracy[[paste0("ncomp = ", iteration)]]

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285 ## change class of numbers into numeric to round and calculate mean

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286 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)

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287 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)

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288 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot

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289 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table

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290 summary_iteration4 = t(summary_iteration3)

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291 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)

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292 summary_oplscv[[count]] = summary_iteration5

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293 count = count+1} ## create list with summary table for each component

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294 summary_oplscv = do.call(rbind, summary_oplscv)

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295 summary_df = as.data.frame(summary_oplscv)

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296 colnames(summary_df) = NULL

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297

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298 ## plots

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299 ## plot to find ncomp with highest accuracy

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300 plot(components, accuracy_vector, ylab = "mean accuracy", type="o", main="Mean accuracy of OPLS classification")

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301 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy

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302 ## one image for each sample/fold, 4 images per page

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303 minimumy = min(coord(msidata.cv.opls)[,2])

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304 maximumy = max(coord(msidata.cv.opls)[,2])

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305 image(msidata.cv.opls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),layout = c(2, 2))

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306

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307 ## print table with summary in pdf

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308 par(opar)

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309 plot(0,type='n',axes=FALSE,ann=FALSE)

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310 title(main="Summary for the different components\n", adj=0.5)

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311 ## 20 rows fits in one page:

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312 if (nrow(summary_df)<=20){

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313 grid.table(summary_df, rows= NULL)

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314 }else{

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315 grid.table(summary_df[1:20,], rows= NULL)

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316 mincount = 21

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317 maxcount = 40

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318 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){

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319 plot(0,type='n',axes=FALSE,ann=FALSE)

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320 if (maxcount <= nrow(summary_df)){

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321 grid.table(summary_df[mincount:maxcount,], rows= NULL)

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322 mincount = mincount+20

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323 maxcount = maxcount+20

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324 }else{### stop last page with last sample otherwise NA in table

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325 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}

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326 }

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327 }

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328

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329 ## optional output as .RData

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330 #if $output_rdata:

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331 save(msidata.cv.opls, file="$classification_rdata")

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332 #end if

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333

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334

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335 ######################## OPLS -analysis ###########################

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336 #elif str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_analysis":

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337 print("OPLS analysis")

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338

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339 ## set variables for components and number of response groups

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340 component = c($type_cond.method_cond.opls_analysis_cond.opls_comp)

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341 number_groups = length(levels(y_vector))

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342

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343

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344 ### opls analysis and coefficients plot

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345 msidata.opls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.opls_analysis_cond.opls_scale, keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew)

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346 plot(msidata.opls, main="OPLS coefficients per m/z")

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347

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348 ### summary table of OPLS

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349 summary_table = summary(msidata.opls)\$accuracy[[paste0("ncomp = ",component)]]

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350 summary_table2 = round(as.numeric(summary_table), digits=2)

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351 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)

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352 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table

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353 summary_table4 = t(summary_table3)

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354 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)

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355 plot(0,type='n',axes=FALSE,ann=FALSE)

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356 grid.table(summary_table5, rows= NULL)

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357

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358 ### image of the best m/z

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359 minimumy = min(coord(msidata)[,2])

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360 maximumy = max(coord(msidata)[,2])

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361 print(image(msidata, mz = topLabels(msidata.opls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), main="best m/z heatmap"))

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362

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363 ## m/z and pixel information output

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364 opls_classes = data.frame(msidata.opls\$classes[[1]])

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365 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))

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366 pixel_names = gsub(" = ", "y_", pixel_names)

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367 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]

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368 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]

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369 opls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, opls_classes)

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370 colnames(opls_classes2) = c("pixel names", "x", "y","predicted condition")

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371

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372 opls_toplabels = topLabels(msidata.opls, n=$type_cond.method_cond.opls_analysis_cond.opls_toplabels)

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373 write.table(opls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")

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374 write.table(opls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")

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375

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376 ## image with predicted classes

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377 prediction_df = cbind(coord(msidata.opls)[,1:2], opls_classes)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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378 colnames(prediction_df) = c("x", "y", "predicted_classes")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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379

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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380 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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381 geom_tile() +

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

382 coord_fixed()+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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383 ggtitle("Predicted condition for each pixel")+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

384 theme_bw()+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

385 theme(text=element_text(family="ArialMT", face="bold", size=15))+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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386 theme(legend.position="bottom",legend.direction="vertical")+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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387 guides(fill=guide_legend(ncol=4,byrow=TRUE))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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388 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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389 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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390 print(prediction_plot)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

391

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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392 ## optional output as .RData

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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393 #if $output_rdata:

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394 save(msidata.opls, file="$classification_rdata")

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395 #end if

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396 #end if

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diff changeset

397

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

398

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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399 ######################## SSC #############################

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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400 #elif str( $type_cond.method_cond.class_method) == "spatialShrunkenCentroids":

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401 print("SSC")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

402

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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403 ######################## SSC - CV #############################

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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404 #if str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_cvapply":

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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405 print("SSC cv")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

406

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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407 ## set variables for components and number of response groups

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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408 number_groups = length(levels(y_vector))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

409

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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410 ## SSC-cvApply:

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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411 msidata.cv.ssc <- cvApply(msidata, .y = y_vector,.fold = fold_vector,.fun = "spatialShrunkenCentroids", r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

412

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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413 ## create table with summary

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

414 count = 1

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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415 summary_ssccv = list()

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

416 accuracy_vector = numeric()

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

417 iteration_vector = character()

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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418 for (iteration in names(msidata.cv.ssc@resultData[[1]][,1])){

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

419

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420 summary_iteration = summary(msidata.cv.ssc)\$accuracy[[iteration]]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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421 ## change class of numbers into numeric to round and calculate mean

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422 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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423 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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424 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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425 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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426 summary_iteration4 = t(summary_iteration3)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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427 summary_iteration5 = cbind(c(iteration, colnames(summary_iteration)), summary_iteration4)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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428 summary_ssccv[[count]] = summary_iteration5

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429 iteration_vector[count] = unlist(strsplit(iteration, "[,]"))[3]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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430 count = count+1} ## create list with summary table for each component

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431 summary_ssccv = do.call(rbind, summary_ssccv)

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432 summary_df = as.data.frame(summary_ssccv)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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433 colnames(summary_df) = NULL

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

434

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

435 ## plot to find parameters with highest accuracy

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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436 plot(c($type_cond.method_cond.ssc_s),accuracy_vector[!duplicated(iteration_vector)], type="o",ylab="Mean accuracy", xlab = "Shrinkage parameter (s)", main="Mean accuracy of SSC classification")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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437 best_params = names(msidata.cv.ssc@resultData[[1]][,1])[which.max(accuracy_vector)] ## find parameters with max. accuracy

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

438 r_value = as.numeric(substring(unlist(strsplit(best_params, ","))[1], 4))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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439 s_value = as.numeric(substring(unlist(strsplit(best_params, ","))[3], 5)) ## remove space

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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440 minimumy = min(coord(msidata.cv.ssc)[,2])

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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441 maximumy = max(coord(msidata.cv.ssc)[,2])

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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442 image(msidata.cv.ssc, model = list( r = r_value, s = s_value ), ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),layout=c(2,2))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

443

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diff changeset

444 ## print table with summary in pdf

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

445 par(opar)

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diff changeset

446 plot(0,type='n',axes=FALSE,ann=FALSE)

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447 title(main="Summary for the different parameters\n", adj=0.5)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

448 ## 20 rows fits in one page:

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diff changeset

449 if (nrow(summary_df)<=20){

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

450 grid.table(summary_df, rows= NULL)

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diff changeset

451 }else{

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

452 grid.table(summary_df[1:20,], rows= NULL)

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diff changeset

453 mincount = 21

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

454 maxcount = 40

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455 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

456 plot(0,type='n',axes=FALSE,ann=FALSE)

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diff changeset

457 if (maxcount <= nrow(summary_df)){

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

458 grid.table(summary_df[mincount:maxcount,], rows= NULL)

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diff changeset

459 mincount = mincount+20

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

460 maxcount = maxcount+20

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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diff changeset

461 }else{### stop last page with last sample otherwise NA in table

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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462 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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463 }

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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464 }

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

465

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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466 ## optional output as .RData

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

467 #if $output_rdata:

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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468 save(msidata.cv.ssc, file="$classification_rdata")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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diff changeset

469 #end if

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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470

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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471 ######################## SSC -analysis ###########################

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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472 #elif str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_analysis":

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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473 print("SSC analysis")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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474

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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475 ## set variables for components and number of response groups

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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476 number_groups = length(levels(y_vector))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

477

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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478 ## SSC analysis and plot

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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479 msidata.ssc <- spatialShrunkenCentroids(msidata, y = y_vector, .fold = fold_vector,

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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480 r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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481 plot(msidata.ssc, mode = "tstatistics", model = list("r" = c($type_cond.method_cond.ssc_r), "s" = c($type_cond.method_cond.ssc_s)))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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482

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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483 ### summary table SSC

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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484 ##############summary_table = summary(msidata.ssc)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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485 summary_table = summary(msidata.ssc)\$accuracy[[names(msidata.ssc@resultData)]]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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486 summary_table2 = round(as.numeric(summary_table), digits=2)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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487 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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488 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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489 summary_table4 = t(summary_table3)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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490 summary_table5 = cbind(c(names(msidata.ssc@resultData),colnames(summary_table)), summary_table4)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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491 plot(0,type='n',axes=FALSE,ann=FALSE)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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492 grid.table(summary_table5, rows= NULL)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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493

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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494 ### image of the best m/z

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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495 minimumy = min(coord(msidata)[,2])

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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496 maximumy = max(coord(msidata)[,2])

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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497 print(image(msidata, mz = topLabels(msidata.ssc)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), main="best m/z heatmap"))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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498

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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499 ## m/z and pixel information output

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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500 ssc_classes = data.frame(msidata.ssc\$classes[[1]])

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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501 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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502 pixel_names = gsub(" = ", "y_", pixel_names)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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503 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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504 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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505 ssc_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, ssc_classes)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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506 colnames(ssc_classes2) = c("pixel names", "x", "y","predicted condition")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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507 ssc_toplabels = topLabels(msidata.ssc, n=$type_cond.method_cond.ssc_analysis_cond.ssc_toplabels)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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508 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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509 write.table(ssc_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

510

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

511 ## image with predicted classes

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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512 prediction_df = cbind(coord(msidata.ssc)[,1:2], ssc_classes)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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513 colnames(prediction_df) = c("x", "y", "predicted_classes")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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514

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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515 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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516 geom_tile() +

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diff changeset

517 coord_fixed()+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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518 ggtitle("Predicted condition for each pixel")+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

519 theme_bw()+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

520 theme(text=element_text(family="ArialMT", face="bold", size=15))+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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521 theme(legend.position="bottom",legend.direction="vertical")+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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522 guides(fill=guide_legend(ncol=4,byrow=TRUE))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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523 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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524 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

525 print(prediction_plot)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

526

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

527

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

528 ## optional output as .RData

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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529 #if $output_rdata:

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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530 save(msidata.ssc, file="$classification_rdata")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

531 #end if

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

532

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

533 #end if

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

534 #end if

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diff changeset

535

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

536

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

537

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

538 ######################## II) Prediction #############################

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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539 #############################################################################

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diff changeset

540

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

541 #elif str($type_cond.type_method) == "prediction":

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

542 print("prediction")

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diff changeset

543

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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544 training_data = loadRData("$type_cond.training_result")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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545

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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546 #if str($type_cond.new_y_values_cond.new_y_values) == "new_response":

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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547 print("new response")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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548

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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549 new_y_tabular = read.delim("$type_cond.new_y_values_cond.new_response_file", header = $type_cond.new_y_values_cond.new_tabular_header, stringsAsFactors = FALSE)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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550 new_y_input = new_y_tabular[,c($type_cond.new_y_values_cond.column_new_x, $type_cond.new_y_values_cond.column_new_y, $type_cond.new_y_values_cond.column_new_response)]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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551 colnames(new_y_input)[1:2] = c("x", "y")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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552 ## merge with coordinate information of msidata

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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553 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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554 colnames(msidata_coordinates)[3] = "pixel_index"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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555 merged_response = merge(msidata_coordinates, new_y_input, by=c("x", "y"), all.x=TRUE)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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556 merged_response[is.na(merged_response)] = "NA"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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557 merged_response = merged_response[order(merged_response\$pixel_index),]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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558 new_y_vector = as.factor(merged_response[,4])

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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559 prediction = predict(training_data,msidata, newy = new_y_vector)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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diff changeset

560

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

561 #else

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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562 prediction = predict(training_data,msidata)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

563 #end if

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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564

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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565 ## m/z and pixel information output

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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566 predicted_classes = data.frame(prediction\$classes[[1]])

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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567 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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568 pixel_names = gsub(" = ", "y_", pixel_names)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

569 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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diff changeset

570 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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571 predicted_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, predicted_classes)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

572 colnames(predicted_classes2) = c("pixel names", "x", "y","predicted condition")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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573 predicted_toplabels = topLabels(prediction, n=$type_cond.predicted_toplabels)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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574 write.table(predicted_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

575 write.table(predicted_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

576

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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parents:

diff changeset

577 ## image with predicted classes

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

578

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

579 prediction_df = cbind(coord(prediction)[,1:2], predicted_classes)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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580 colnames(prediction_df) = c("x", "y", "predicted_classes")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

581

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galaxyp

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diff changeset

582 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

583 geom_tile() +

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

584 coord_fixed()+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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diff changeset

585 ggtitle("Predicted condition for each pixel")+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

586 theme_bw()+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

587 theme(text=element_text(family="ArialMT", face="bold", size=15))+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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diff changeset

588 theme(legend.position="bottom",legend.direction="vertical")+

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

589 guides(fill=guide_legend(ncol=4,byrow=TRUE))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

590 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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591 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

592 print(prediction_plot)

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diff changeset

593

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

594 ## Summary table prediction

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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595 summary_table = summary(prediction)\$accuracy[[names(prediction@resultData)]]

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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596 summary_table2 = round(as.numeric(summary_table), digits=2)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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597 summary_matrix = matrix(summary_table2, nrow=4, ncol=ncol(summary_table))

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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598 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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599 summary_table4 = t(summary_table3)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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600 summary_table5 = cbind(c(names(prediction@resultData),colnames(summary_table)), summary_table4)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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601 plot(0,type='n',axes=FALSE,ann=FALSE)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

602 grid.table(summary_table5, rows= NULL)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

603

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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604 ## optional output as .RData

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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605 #if $output_rdata:

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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606 msidata = prediction

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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607 save(msidata, file="$classification_rdata")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

608 #end if

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diff changeset

609

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

610 #end if

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

611

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

612 dev.off()

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613

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diff changeset

614 }else{

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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615 print("Inputfile has no intensities > 0 or contains NA values")

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

616 dev.off()

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617 }

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618

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diff changeset

619

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diff changeset

620 ]]></configfile>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

621 </configfiles>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

622 <inputs>

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diff changeset

623 <expand macro="reading_msidata"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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diff changeset

624 <conditional name="type_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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625 <param name="type_method" type="select" label="Analysis step to perform">

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626 <option value="training" selected="True">training</option>

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parents:

diff changeset

627 <option value="prediction">prediction</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

628 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

629 <when value="training">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

630

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

631 <param name="annotation_file" type="data" format="tabular" label="Load tabular file with pixel coordinates and their classes"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

632 help="Three or four columns: x values, y values, response values, optionally fold values"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

633 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

634 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

635 <param name="column_response" data_ref="annotation_file" label="Column with response (condition) values" type="data_column" help="This is the condition (pixel group) which will be classified"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

636 <param name="column_fold" data_ref="annotation_file" optional="True" label="Column with fold values - only neccessary for cvapply" type="data_column" help="Each fold must contain pixels of all response groups and is used for cross validation"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

637 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

638

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

639 <conditional name="method_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

640 <param name="class_method" type="select" label="Select the method for classification">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

641 <option value="PLS" selected="True">PLS-DA</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

642 <option value="OPLS">OPLS-DA</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

643 <option value="spatialShrunkenCentroids">spatial shrunken centroids</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

644 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

645 <when value="PLS">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

646

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

647 <conditional name="analysis_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

648 <param name="PLS_method" type="select" label="Crossvalidation or analysis">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

649 <option value="cvapply" selected="True">cvApply</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

650 <option value="PLS_analysis">PLS-DA analysis</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

651 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

652 <when value="cvapply">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

653 <param name="plscv_comp" type="text" value="1:2"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

654 label="The number of PLS-DA components" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5)">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

655 <expand macro="sanitizer_multiple_digits"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

656 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

657 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

658 <when value="PLS_analysis">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

659 <param name="pls_comp" type="integer" value="5"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

660 label="The optimal number of PLS-DA components as indicated by cross-validations" help="Run cvApply first to optain optiaml number of PLS-DA components"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

661 <param name="pls_scale" type="boolean" label="Data scaling" truevalue="TRUE" falsevalue="FALSE"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

662 <param name="pls_toplabels" type="integer" value="100"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

663 label="Number of toplabels (m/z features) which should be written in tabular output"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

664 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

665 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

666 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

667

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

668 <when value="OPLS">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

669

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

670 <conditional name="opls_analysis_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

671 <param name="opls_method" type="select" label="Analysis step to perform">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

672 <option value="opls_cvapply" selected="True">cvApply</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

673 <option value="opls_analysis">OPLS-DA analysis</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

674 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

675

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

676 <when value="opls_cvapply">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

677 <param name="opls_cvcomp" type="text" value="1:2"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

678 label="The number of OPLS-DA components" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5)">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

679 <expand macro="sanitizer_multiple_digits"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

680 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

681 <param name="xnew_cv" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Keep new matrix"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

682 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

683

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

684 <when value="opls_analysis">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

685 <param name="opls_comp" type="integer" value="5"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

686 label="The optimal number of OPLS-DA components as indicated by cross-validations" help="Run cvApply first to optain optiaml number of OPLS-DA components"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

687 <param name="xnew" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Keep new matrix"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

688 <param name="opls_scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Data scaling"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

689 <param name="opls_toplabels" type="integer" value="100"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

690 label="Number of toplabels (m/z features) which should be written in tabular output"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

691 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

692 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

693 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

694

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

695 <when value="spatialShrunkenCentroids">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

696 <conditional name="ssc_analysis_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

697 <param name="ssc_method" type="select" label="Analysis step to perform">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

698 <option value="ssc_cvapply" selected="True">cvApply</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

699 <option value="ssc_analysis">spatial shrunken centroids analysis</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

700 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

701 <when value="ssc_cvapply"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

702

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

703 <when value="ssc_analysis">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

704 <param name="ssc_toplabels" type="integer" value="100"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

705 label="Number of toplabels (m/z features) which should be written in tabular output"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

706 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

707 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

708 <param name="ssc_r" type="text" value="2"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

709 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5)">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

710 <expand macro="sanitizer_multiple_digits"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

711 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

712 <param name="ssc_s" type="text" value="2"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

713 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5)">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

714 <expand macro="sanitizer_multiple_digits"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

715 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

716 <param name="ssc_kernel_method" type="select" display="radio" label = "The method to use to calculate the spatial smoothing kernels for the embedding. The 'gaussian' method refers to spatially-aware (SA) weights, and 'adaptive' refers to spatially-aware structurally-adaptive (SASA) weights">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

717 <option value="gaussian">gaussian</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

718 <option value="adaptive" selected="True">adaptive</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

719 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

720

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

721 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

722 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

723 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

724

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

725 <when value="prediction">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

726 <param name="training_result" type="data" format="rdata" label="Result from previous classification training"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

727 <param name="predicted_toplabels" type="integer" value="100"

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

728 label="Number of toplabels (m/z features) which should be written in tabular output"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

729 <conditional name="new_y_values_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

730 <param name="new_y_values" type="select" label="Should new response values be used">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

731 <option value="no_new_response" selected="True">old response should be used</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

732 <option value="new_response">load new response from tabular file</option>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

733 </param>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

734 <when value="no_new_response"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

735 <when value="new_response">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

736 <param name="new_response_file" type="data" format="tabular" label="Load tabular file with pixel coordinates and the new response"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

737 <param name="column_new_x" data_ref="new_response_file" label="Column with x values" type="data_column"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

738 <param name="column_new_y" data_ref="new_response_file" label="Column with y values" type="data_column"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

739 <param name="column_new_response" data_ref="new_response_file" label="Column with new response values" type="data_column"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

740 <param name="new_tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

741 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

742 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

743 </when>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

744 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

745 <param name="output_rdata" type="boolean" label="Results as .RData output" help="Can be used to generate a classification prediction on new data"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

746 </inputs>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

747 <outputs>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

748 <data format="pdf" name="classification_images" from_work_dir="classificationpdf.pdf" label = "${tool.name} on ${on_string}"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

749 <data format="tabular" name="mzfeatures" label="${tool.name} on ${on_string}: features"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

750 <data format="tabular" name="pixeloutput" label="${tool.name} on ${on_string}: pixels"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

751 <data format="rdata" name="classification_rdata" label="${tool.name} on ${on_string}: results.RData">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

752 <filter>output_rdata</filter>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

753 </data>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

754 </outputs>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

755 <tests>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

756 <test expect_num_outputs="3">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

757 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

758 <conditional name="type_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

759 <param name="type_method" value="training"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

760 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

761 <param name="column_x" value="1"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

762 <param name="column_y" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

763 <param name="column_response" value="4"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

764 <param name="column_fold" value="3"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

765 <param name="tabular_header" value="False"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

766 <conditional name="method_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

767 <param name="class_method" value="PLS"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

768 <conditional name="analysis_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

769 <param name="PLS_method" value="cvapply"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

770 <param name="plscv_comp" value="2:4"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

771 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

772 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

773 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

774 <output name="mzfeatures" file="features_test1.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

775 <output name="pixeloutput" file="pixels_test1.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

776 <output name="classification_images" file="test1.pdf" compare="sim_size" delta="2000"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

777 </test>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

778

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

779 <test expect_num_outputs="4">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

780 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

781 <conditional name="type_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

782 <param name="type_method" value="training"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

783 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

784 <param name="column_x" value="1"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

785 <param name="column_y" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

786 <param name="column_response" value="4"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

787 <param name="tabular_header" value="False"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

788 <conditional name="method_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

789 <param name="class_method" value="PLS"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

790 <conditional name="analysis_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

791 <param name="PLS_method" value="PLS_analysis"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

792 <param name="pls_comp" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

793 <param name="pls_scale" value="TRUE"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

794 <param name="pls_toplabels" value="100"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

795 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

796 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

797 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

798 <param name="output_rdata" value="True"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

799 <output name="mzfeatures" file="features_test2.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

800 <output name="pixeloutput" file="pixels_test2.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

801 <output name="classification_images" file="test2.pdf" compare="sim_size"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

802 <output name="classification_rdata" file="test2.rdata" compare="sim_size"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

803 </test>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

804

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

805 <test expect_num_outputs="3">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

806 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

807 <conditional name="type_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

808 <param name="type_method" value="training"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

809 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

810 <param name="column_x" value="1"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

811 <param name="column_y" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

812 <param name="column_response" value="4"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

813 <param name="column_fold" value="3"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

814 <param name="tabular_header" value="False"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

815 <conditional name="method_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

816 <param name="class_method" value="OPLS"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

817 <conditional name="opls_analysis_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

818 <param name="opls_method" value="opls_cvapply"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

819 <param name="opls_cvcomp" value="1:2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

820 <param name="xnew_cv" value="FALSE"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

821 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

822 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

823 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

824 <output name="mzfeatures" file="features_test3.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

825 <output name="pixeloutput" file="pixels_test3.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

826 <output name="classification_images" file="test3.pdf" compare="sim_size"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

827 </test>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

828

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

829 <test expect_num_outputs="4">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

830 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

831 <conditional name="type_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

832 <param name="type_method" value="training"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

833 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

834 <param name="column_x" value="1"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

835 <param name="column_y" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

836 <param name="column_response" value="4"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

837 <param name="tabular_header" value="False"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

838 <conditional name="method_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

839 <param name="class_method" value="OPLS"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

840 <conditional name="opls_analysis_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

841 <param name="opls_method" value="opls_analysis"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

842 <param name="opls_comp" value="3"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

843 <param name="xnew" value="FALSE"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

844 <param name="opls_scale" value="FALSE"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

845 <param name="opls_toplabels" value="100"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

846 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

847 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

848 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

849 <param name="output_rdata" value="True"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

850 <output name="mzfeatures" file="features_test4.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

851 <output name="pixeloutput" file="pixels_test4.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

852 <output name="classification_images" file="test4.pdf" compare="sim_size"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

853 <output name="classification_rdata" file="test4.rdata" compare="sim_size"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

854 </test>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

855

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

856 <test expect_num_outputs="3">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

857 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

858 <conditional name="type_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

859 <param name="type_method" value="training"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

860 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

861 <param name="column_x" value="1"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

862 <param name="column_y" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

863 <param name="column_response" value="3"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

864 <param name="column_fold" value="4"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

865 <param name="tabular_header" value="False"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

866 <conditional name="method_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

867 <param name="class_method" value="spatialShrunkenCentroids"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

868 <conditional name="ssc_analysis_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

869 <param name="ssc_method" value="ssc_cvapply"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

870 <param name="ssc_r" value="1:2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

871 <param name="ssc_s" value="2:3"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

872 <param name="ssc_kernel_method" value="adaptive"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

873 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

874 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

875 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

876 <output name="mzfeatures" file="features_test5.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

877 <output name="pixeloutput" file="pixels_test5.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

878 <output name="classification_images" file="test5.pdf" compare="sim_size"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

879 </test>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

880

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

881 <test expect_num_outputs="4">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

882 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

883 <conditional name="type_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

884 <param name="type_method" value="training"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

885 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

886 <param name="column_x" value="1"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

887 <param name="column_y" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

888 <param name="column_response" value="4"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

889 <conditional name="method_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

890 <param name="class_method" value="spatialShrunkenCentroids"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

891 <conditional name="ssc_analysis_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

892 <param name="ssc_method" value="ssc_analysis"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

893 <param name="ssc_toplabels" value="20"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

894 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

895 <param name="ssc_r" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

896 <param name="ssc_s" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

897 <param name="ssc_kernel_method" value="adaptive"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

898 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

899 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

900 <param name="output_rdata" value="True"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

901 <output name="mzfeatures" file="features_test6.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

902 <output name="pixeloutput" file="pixels_test6.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

903 <output name="classification_images" file="test6.pdf" compare="sim_size"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

904 <output name="classification_rdata" file="test6.rdata" compare="sim_size" />

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

905 </test>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

906

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

907 <test expect_num_outputs="4">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

908 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

909 <conditional name="type_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

910 <param name="type_method" value="prediction"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

911 <param name="training_result" value="test2.rdata" ftype="rdata"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

912 <conditional name="new_y_values_cond">

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

913 <param name="new_y_values" value="new_response"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

914 <param name="new_response_file" value="pixel_annotation_file1.tabular" ftype="tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

915 <param name="column_new_x" value="1"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

916 <param name="column_new_y" value="2"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

917 <param name="column_new_response" value="4"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

918 <param name="new_tabular_header" value="False"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

919 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

920 </conditional>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

921 <param name="output_rdata" value="True"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

922 <output name="mzfeatures" file="features_test7.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

923 <output name="pixeloutput" file="pixels_test7.tabular"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

924 <output name="classification_images" file="test7.pdf" compare="sim_size"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

925 <output name="classification_rdata" file="test7.rdata" compare="sim_size" />

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

926 </test>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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diff changeset

927 </tests>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

928 <help>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

929 <![CDATA[

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

930

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

931

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

932 @CARDINAL_DESCRIPTION@

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

933

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

934 -----

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

935

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

936 This tool provides three different Cardinal functions for supervised classification of mass-spectrometry imaging data.

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

937

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

938 @MSIDATA_INPUT_DESCRIPTION@

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

939 - For training: tabular file with condition and fold for each pixel: Two columns for pixel coordinates (x and y values); one column with the condition for the pixel, which will be used for classification; for the cross validation (cvapply) another column with a fold is necessary, each fold must contain pixels of all response groups and is used for cross validation. Condition and fold columns are treated as factor to perform discriminant analysis (also when numeric values are provided).

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

940

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

941 ::

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

942

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

943 x_coord y_coord condition fold

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

944 1 1 A f1

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

945 2 1 A f2

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

946 3 1 A f3

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

947 1 2 B f1

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

948 2 2 B f2

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

949 3 2 B f3

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

950 ...

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

951 ...

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

952

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

953

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

954 - For prediction: RData output from previous classification run is needed as input, optionally new response values can be loaded with a tabular file containing x values, y values and the response

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

955

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

956

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

957 **Options**

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

958

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

959 - PLS-DA: partial least square discriminant analysis

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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diff changeset

960 - O-PLS-DA: Orthogonal partial least squares discriminant analysis

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

961 - Spatial shrunken centroids

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

962

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

parents:

diff changeset

963 **Tips**

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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diff changeset

964

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

galaxyp

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965 - The classification function will only run on files with valid intensity values (NA are not allowed)

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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966 - Only a single input file is accepted, several files have to be combined previously, for example with the msi_combine tool.

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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967

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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968

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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969 **Output**

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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970

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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971 - Pdf with the heatmaps and plots for the classification

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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972 - Tabular file with information on m/z features and pixels: toplabels/classes

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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973 - Optional: RData output that can be used to predict new data or to explore the results more deeply with the Cardinal package in R

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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974

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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975 ]]>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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976 </help>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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977 <expand macro="citations"/>

7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

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978 </tool>

Mercurial > repos > galaxyp > cardinal_classification

annotate classification.xml @ 0:7d1500ecbda9 draft