Mercurial > repos > iuc > ggplot2_heatmap

annotate ggplot2_heatmap.xml @ 8:8b8a26a5fdf2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
author iuc
date Thu, 15 May 2025 13:01:32 +0000
parents 48fc850095ba
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents: 7
diff changeset
1 <tool id="ggplot2_heatmap" name="Heatmap w ggplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
2 <macros>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
3 <import>macros.xml</import>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
4 </macros>
7
48fc850095ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
iuc
parents: 6
diff changeset
5 <expand macro="bio_tools"/>
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
6 <requirements>
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
7 <requirement type="package" version="1.1.1">r-cowplot</requirement>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
8 <requirement type="package" version="0.4.5">r-egg</requirement>
6
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
9 <requirement type="package" version="0.1.23">r-ggdendro</requirement>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
10 <requirement type="package" version="1.0.10">r-dplyr</requirement>
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
11 <requirement type="package" version="1.4.4">r-reshape2</requirement>
6
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
12 <requirement type="package" version="2.1.0">r-svglite</requirement>
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
13 </requirements>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
14 <command detect_errors="exit_code"><![CDATA[
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
15 cat '$script' &&
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
16 Rscript '$script'
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
17 ]]></command>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
18 <configfiles>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
19 <configfile name="script"><![CDATA[
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
20 @R_INIT@
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
21
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
22 ## Import library
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
23
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
24 library(ggplot2)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
25 library(cowplot)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
26 library(egg)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
27 library(dplyr)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
28 library(ggdendro)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
29 library(reshape2)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
30
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
31 input <- '$input1'
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
32 header <- ${inputdata.header}
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
33 rowname_index <- as.integer('$inputdata.row_names_index')
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
34
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
35 transform <- '$adv.transform'
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
36
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
37 ## read table with or with out header or row_names
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
38 if(rowname_index > 0){
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
39 df <- read.table(input, header = header, row.names = rowname_index, sep = "\t")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
40 }else{
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
41 df <- read.table(input, header = header, sep = "\t")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
42 }
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
43
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
44 hclust_fun = function(x) hclust(x, method="complete")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
45 dist_fun = function(x) dist(x, method="maximum")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
46 distfun=dist_fun
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
47 hclustfun=hclust_fun
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
48
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
49 plot_mat <- df
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
50
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
51 ## transform dataset
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
52 if(transform == "log2"){
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
53 plot_mat <- log2(plot_mat)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
54 cat("\n ", transform, " transformed")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
55 }else if(transform == "log2plus1"){
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
56 plot_mat <- log2(plot_mat+1)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
57 cat("\n ", transform, " transformed")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
58 }else if(transform == "log10"){
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
59 plot_mat <- log10(plot_mat)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
60 cat("\n ", transform, " transformed")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
61 }else if(transform == "log10plus1"){
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
62 plot_mat <- log10(plot_mat+1)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
63 cat("\n ", transform, " transformed")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
64 }else{
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
65 plot_mat <- plot_mat
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
66 }
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
67
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
68 #if $adv.colorscheme == "whrd"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
69 colorscale = scale_fill_gradient(low="white", high="red", guide="colorbar")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
70 #elif $adv.colorscheme == "whblu"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
71 colorscale = scale_fill_gradient(low="white", high="blue", guide="colorbar")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
72 #elif $adv.colorscheme == "blwhre"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
73 colorscale = scale_fill_gradient2(low="blue", mid="white", high="red", guide="colorbar")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
74 #end if
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
75
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
76 plot_mat["rows"] <- row.names(plot_mat)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
77 plot_mat.melt <- melt(plot_mat, id.vars = "rows")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
78 names(plot_mat.melt)[2] <- "cols"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
79
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
80 #if $adv.cluster:
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
81
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
82 plot_mat.dendo <- as.dendrogram(hclust(d = dist(x = subset(plot_mat, select = -rows))))
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
83
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
84 plot_mat.dendo.order <- order.dendrogram(plot_mat.dendo)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
85
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
86 gg_rows = ggdendrogram(data = plot_mat.dendo, rotate = FALSE) +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
87 theme(axis.text.y = element_text(size = 6), axis.text.x = element_blank())
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
88
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
89 plot_mat.melt[,"rows"] <- factor(x = plot_mat.melt[,"rows"],
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
90 levels = unique(plot_mat.melt[,"rows"])[plot_mat.dendo.order],
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
91 ordered = TRUE)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
92
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
93 plot_mat.dendo <- as.dendrogram(hclust(d = dist(x = t(subset(plot_mat, select = -rows)))))
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
94 plot_mat.dendo.order <- order.dendrogram(plot_mat.dendo)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
95
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
96 gg_cols = ggdendrogram(data = plot_mat.dendo, rotate = TRUE) +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
97 theme(axis.text.x = element_text(size = 6), axis.text.y = element_blank())
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
98
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
99 plot_mat.melt[,"cols"] <- factor(x = plot_mat.melt[,"cols"],
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
100 levels = unique(plot_mat.melt[,"cols"])[plot_mat.dendo.order],
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
101 ordered = TRUE)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
102
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
103 ## plot the heatmap
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
104 gg_hm = plot_mat.melt %>%
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
105 ggplot(aes(x = rows, y = cols, fill = value)) +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
106 geom_tile() +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
107 theme(legend.position = "bottom", axis.title.x = element_blank(), axis.title.y = element_blank(),
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
108 axis.text.x = element_text(angle = 90, hjust = 1)) +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
109 colorscale
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
110
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
111 gg_empty = plot_mat.melt %>%
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
112 ggplot(aes(x = cols, y = value)) +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
113 geom_blank() +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
114 theme(axis.text = element_blank(),
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
115 axis.title = element_blank(),
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
116 line = element_blank(),
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
117 panel.background = element_blank())
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
118
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
119 plot_out <- ggarrange(
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
120 gg_rows, gg_empty, gg_hm, gg_cols,
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
121 nrow = 2, ncol = 2, widths = c(3, 1), heights = c(1, 3), newpage =F)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
122
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
123 #else
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
124
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
125 ## plot the heatmap
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
126 gg_hm = plot_mat.melt %>%
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
127 ggplot(aes(x = rows, y = cols, fill = value)) +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
128 geom_tile() + ggtitle('$title') +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
129 theme(legend.position = "bottom", axis.title.x = element_blank(), axis.title.y = element_blank(), axis.text.x = element_text(angle = 90, hjust = 1)) +
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
130 colorscale
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
131
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
132 plot_out <- gg_hm
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
133
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
134 #end if
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
135
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
136 @SAVE_OUTPUT@
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
137 ]]></configfile>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
138 </configfiles>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
139 <inputs>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
140 <expand macro="read_complex_input"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
141 <expand macro="title"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
142 <!-- Advanced Options -->
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
143 <section name="adv" title="Advanced Options" expanded="false">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
144 <expand macro="transform" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
145 <param name="cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable data clustering" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
146 <param name="colorscheme" type="select" label="Heatmap colorscheme" >
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
147 <option value="whrd" selected="true">White to red</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
148 <option value="whblu">White to blue</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
149 <option value="blwhre">Blue to white to red</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
150 </param>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
151 </section>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
152 <!-- Output Options -->
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
153 <section name="out" title="Output Options" expanded="true">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
154 <expand macro="dimensions" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
155 </section>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
156 </inputs>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
157 <outputs>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
158 <expand macro="additional_output" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
159 </outputs>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
160 <tests>
7
48fc850095ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
iuc
parents: 6
diff changeset
161 <test expect_num_outputs="2">
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
162 <param name="input1" value="mtcars.txt" ftype="tabular"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
163 <conditional name="inputdata">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
164 <param name="input_type" value="with_header_rownames"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
165 <param name="header" value="TRUE"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
166 <param name="row_names_index" value="1"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
167 <param name="sample_name_orientation" value="TRUE"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
168 </conditional>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
169 <param name="transform" value="log10plus1"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
170 <param name="cluster" value="true"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
171 <param name="colorscheme" value="blwhre"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
172 <param name="additional_output_format" value="pdf"/>
7
48fc850095ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
iuc
parents: 6
diff changeset
173 <output name="output2" file="ggplot_heatmap_result1.pdf" ftype="pdf" compare="sim_size"/>
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
174 </test>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
175 </tests>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
176 <help><![CDATA[
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
177 This tool will generate a clustered heatmap of your data. More customization options will be added, for now the heatmap uses a red coloring scheme and clustering is performed using the "maximum" similarity measure and the "complete" hierarchical clustering measure.
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
178
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
179 Input data should have row labels in the first column and column labels. For example, the row labels (the first column) should represent gene IDs and the column labels should represent sample IDs.
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
180 ]]></help>
7
48fc850095ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
iuc
parents: 6
diff changeset
181 <expand macro="citations"/>
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
182 </tool>