msi_spectra_plot: msi_spectra_plots.xml comparison

comparison msi_spectra_plots.xml @ 4:dcf79af72c8f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5

author	galaxyp
date	Tue, 19 Jun 2018 18:06:46 -0400
parents	693a8efdfdeb
children	bc931322e4d6

comparison

equal deleted inserted replaced

-:693a8efdfdeb
+:dcf79af72c8f
-<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.1">
+<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.2">
 <description>
 mass spectrometry imaging mass spectra plots
 </description>
 <requirements>
 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
 <requirement type="package" version="2.2.1">r-gridextra</requirement>
+<requirement type="package" version="2.2.1">r-ggplot2</requirement>
+<requirement type="package" version="0.5.0">r-scales</requirement>
 </requirements>
 <command detect_errors="exit_code">
 <![CDATA[
 #if $infile.ext == 'imzml'
 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
 ################################# load libraries and read file #################
 library(Cardinal)
 library(gridExtra)
+library(ggplot2)
-## Read MALDI Imaging dataset
+library(scales)
 #if $infile.ext == 'imzml'
-msidata = readImzML('infile')
+msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units")
 #elif $infile.ext == 'analyze75'
 msidata = readAnalyze('infile')
 #else
 load('infile.RData')
 #end if
 TICs = colSums(spectra(msidata)[])
 NumemptyTIC = sum(TICs == 0)
 ## Processing informations
 processinginfo = processingData(msidata)
-centroidedinfo = processinginfo@centroided # TRUE or FALSE
+centroidedinfo = processinginfo@centroided
-## if TRUE write processinginfo if no write FALSE
+## if TRUE write processinginfo if FALSE write FALSE
 ## normalization
 if (length(processinginfo@normalization) == 0) {
 normalizationinfo='FALSE'
 } else {
 } else {
 peakpickinginfo=processinginfo@peakPicking
 }
 properties = c("Number of m/z features",
-"Range of m/z values [Da]",
+"Range of m/z values",
 "Number of pixels",
 "Range of x coordinates",
 "Range of y coordinates",
 "Range of intensities",
 "Median of intensities",
 ############################# sample pixel ################################
 ###########################################################################
 #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
-print("sample_pixel")
+print("sample pixels")
 ##################### I) Sample: plot full mass spectrum ##############
-plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=TRUE, col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE)
+## coloured plot with mean over all spectra for combined_sample, otherwise only 1 black plot
+if (!is.null(levels(msidata\$combined_sample))){
+print("combined samples")
+## overview plot over combined sample, in case more than 10 combined_samples legend has to be taken from this plot
+number_combined = length(levels(msidata\$combined_sample))
+## the more combined_samples a file has the smaller will be the legend
+if (number_combined<20){
+legend_size = 10
+}else if (number_combined>20 && number_combined<40){
+legend_size = 9
+}else if (number_combined>40 && number_combined<60){
+legend_size = 8
+}else if (number_combined>60 && number_combined<100){
+legend_size = 7
+}else{
+legend_size = 6
+}
+position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample)
+colnames(position_df)[3] = "sample_name"
+combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
+geom_tile() +
+coord_fixed()+
+ggtitle("Spatial orientation of combined data")+
+theme_bw()+
+theme(plot.title = element_text(hjust = 0.5))+
+theme(text=element_text(family="ArialMT", face="bold", size=12))+
+theme(legend.position="bottom",legend.direction="vertical")+
+theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
+guides(fill=guide_legend(ncol=5,byrow=TRUE))
+coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
+coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
+for(file_count in 1:nrow(coord_labels))
+{combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
+y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
+print(combine_plot)
+## print legend only for less than 10 samples
+if (length(levels(msidata\$combined_sample)) < 10){
+key_legend = TRUE
+}else{key_legend = FALSE}
+plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=key_legend, col=hue_pal()(length(levels(msidata\$combined_sample))),superpose=TRUE)
+}else{
+plot(msidata, pixel=1:ncol(msidata), key=TRUE)}
 ##################### II) Sample: plot zoom-in mass spectrum ##########
 #if $pixel_conditional.zoomed_sample:
 #for $token in $pixel_conditional.zoomed_sample:
+print("zoomed sample pixels")
 minmasspixel = features(msidata, mz=$token.xlimmin)
 maxmasspixel = features(msidata, mz=$token.xlimmax)
-plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),
+## coloured plot with mean over all spectra for combined_sample, otherwise only 1 black plot
-xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$combined_sample,
+if (!is.null(levels(msidata\$combined_sample))){
-key=TRUE,col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE)
+print("combined samples")
+plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),
+xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$combined_sample,
+key=key_legend,col=hue_pal()(length(levels(msidata\$combined_sample))), superpose=TRUE)
+}else{
+plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))}
 #end for
 #end if
+if (!is.null(levels(msidata\$combined_sample))){
 pixeldf = data.frame(table(msidata\$combined_sample))
+}else{
+pixeldf = data.frame("$filename", ncol(msidata))}
 colnames(pixeldf) = c("sample name", "number of pixels")
 #end if
+### overview table of pixels or samples:
 plot(0,type='n',axes=FALSE,ann=FALSE)
 title(main="Overview of chosen pixel:")
-grid.table(pixeldf, rows= NULL)
+### for more than 20 combined samples print only 20 samples per page:
+if (is.null(levels(msidata\$combined_sample))){
+grid.table(pixeldf, rows= NULL)
+}else if (length(levels(msidata\$combined_sample)) <= 20){
+grid.table(pixeldf, rows= NULL)
+}else{
+grid.table(pixeldf[1:20,], rows= NULL)
+mincount = 21
+maxcount = 40
+for (count20 in 1:(ceiling(nrow(pixeldf)/20)-1)){
+plot(0,type='n',axes=FALSE,ann=FALSE)
+if (maxcount <= nrow(pixeldf)){
+grid.table(pixeldf[mincount:maxcount,], rows= NULL)
+mincount = mincount+20
+maxcount = maxcount+20
+}else{### stop last page with last sample otherwise NA in table
+grid.table(pixeldf[mincount:nrow(pixeldf),], rows= NULL)}
+}
+}
 dev.off()
 }else{
 print("Inputfile has no intensities > 0")
 ]]></configfile>
 </configfiles>
 <inputs>
 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
+<param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
+<param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm">
+<option value="mz" >mz</option>
+<option value="ppm" selected="True" >ppm</option>
+</param>
 <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/>
 <conditional name="pixel_conditional">
 <param name="pixel_type" type="select" label="Select if you want to plot the mass spectrum of a single pixel or of all pixels of a sample">
 <option value="single_pixel" selected="True">Single pixel</option>
 <option value="sample_pixel">All pixels of a sample</option>
 <repeat name="repeatpixel">
 <param name="plusminusinDalton" value="0.25"/>
 <param name="inputx" value="2"/>
 <param name="inputy" value="2"/>
 </repeat>
 </conditional>
 <output name="plots" file="Plot_analyze75.pdf" compare="sim_size" delta="20000"/>
+</test>
+<test>
+<param name="infile" value="" ftype="analyze75">
+<composite_data value="Analyze75.hdr"/>
+<composite_data value="Analyze75.img"/>
+<composite_data value="Analyze75.t2m"/>
+</param>
+<conditional name="pixel_conditional">
+<param name="pixel_type" value="sample_pixel"/>
+<repeat name="zoomed_sample">
+<param name="xlimmin" value="1250"/>
+<param name="xlimmax" value="1270"/>
+</repeat>
+</conditional>
+<output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size" delta="20000"/>
 </test>
 <test>
 <param name="infile" value="123_combined.RData" ftype="rdata"/>
 <conditional name="pixel_conditional">
 <param name="pixel_type" value="sample_pixel"/>
 <repeat name="zoomed_sample">
 <param name="xlimmin" value="350"/>
 <param name="xlimmax" value="360"/>
 </repeat>
 </conditional>
 <output name="plots" file="Plot_rdata.pdf" compare="sim_size" delta="20000"/>
 </test>
 <test>
 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
-<param name="plusminusinDalton" value="0.1"/>
+<conditional name="pixel_conditional">
-<param name="inputx" value="1"/>
+<param name="pixel_type" value="single_pixel"/>
-<param name="inputy" value="1"/>
+<repeat name="repeatpixel">
-<repeat name="repeatpixel">
+<param name="plusminusinDalton" value="0.1"/>
-<param name="plusminusinDalton" value="0.25"/>
+<param name="inputx" value="1"/>
-<param name="inputx" value="2"/>
+<param name="inputy" value="1"/>
-<param name="inputy" value="2"/>
+</repeat>
-<repeat name="zoomedplot">
+</conditional>
-<param name="xlimmin" value="1000"/>
-<param name="xlimmax" value="1050"/>
-</repeat>
-</repeat>
 <output name="plots" file="Plot_empty_spectra.pdf" compare="sim_size" delta="20000"/>
 </test>
 </tests>
 <help><![CDATA[
 - "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates
 - Enter the x and y coordinates of your pixel of interest
 - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type.
 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
-- "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each subfile
+- "All pixels of a sample": Returns a full average mass spectrum plot with different colours for the sample/each combined sample
-- This option only works on files that have previosly been combined in the combine tool
 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
 Output:
 - Pdf with the selected mass spectra plots and additional control plots

Mercurial > repos > galaxyp > msi_spectra_plot

comparison msi_spectra_plots.xml @ 4:dcf79af72c8f draft