annotate ggplot2_heatmap.xml @ 5:d3a9e32672ec draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
author iuc
date Tue, 23 Nov 2021 07:57:24 +0000
parents 391a4cc45fea
children 10515715c940
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d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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1 <tool id="ggplot2_heatmap" name="Heatmap w ggplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
4
391a4cc45fea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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2 <expand macro="bio_tools"/>
0
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3 <macros>
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4 <import>macros.xml</import>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="1.1.1">r-cowplot</requirement>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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8 <requirement type="package" version="0.4.5">r-egg</requirement>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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9 <requirement type="package" version="0.1.22">r-ggdendro</requirement>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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10 <requirement type="package" version="1.0.7">r-dplyr</requirement>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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11 <requirement type="package" version="1.4.4">r-reshape2</requirement>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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12 <requirement type="package" version="2.0.0">r-svglite</requirement>
0
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13 </requirements>
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14 <command detect_errors="exit_code"><![CDATA[
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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15 cat '$script' &&
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16 Rscript '$script'
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17 ]]></command>
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18 <configfiles>
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19 <configfile name="script"><![CDATA[
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20 @R_INIT@
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21
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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22 ## Import library
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23
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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24 library(ggplot2)
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25 library(cowplot)
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26 library(egg)
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27 library(dplyr)
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28 library(ggdendro)
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29 library(reshape2)
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30
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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31 input <- '$input1'
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32 header <- ${inputdata.header}
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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33 rowname_index <- as.integer('$inputdata.row_names_index')
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34
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35 transform <- '$adv.transform'
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36
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37 ## read table with or with out header or row_names
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38 if(rowname_index > 0){
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39 df <- read.table(input, header = header, row.names = rowname_index, sep = "\t")
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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40 }else{
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41 df <- read.table(input, header = header, sep = "\t")
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42 }
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43
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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44 hclust_fun = function(x) hclust(x, method="complete")
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45 dist_fun = function(x) dist(x, method="maximum")
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46 distfun=dist_fun
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47 hclustfun=hclust_fun
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48
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49 plot_mat <- df
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50
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51 ## transform dataset
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52 if(transform == "log2"){
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53 plot_mat <- log2(plot_mat)
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54 cat("\n ", transform, " transformed")
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55 }else if(transform == "log2plus1"){
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56 plot_mat <- log2(plot_mat+1)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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57 cat("\n ", transform, " transformed")
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58 }else if(transform == "log10"){
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59 plot_mat <- log10(plot_mat)
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60 cat("\n ", transform, " transformed")
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61 }else if(transform == "log10plus1"){
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62 plot_mat <- log10(plot_mat+1)
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63 cat("\n ", transform, " transformed")
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64 }else{
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65 plot_mat <- plot_mat
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66 }
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67
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68 #if $adv.colorscheme == "whrd"
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69 colorscale = scale_fill_gradient(low="white", high="red", guide="colorbar")
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70 #elif $adv.colorscheme == "whblu"
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71 colorscale = scale_fill_gradient(low="white", high="blue", guide="colorbar")
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72 #elif $adv.colorscheme == "blwhre"
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73 colorscale = scale_fill_gradient2(low="blue", mid="white", high="red", guide="colorbar")
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74 #end if
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75
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76 plot_mat["rows"] <- row.names(plot_mat)
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77 plot_mat.melt <- melt(plot_mat, id.vars = "rows")
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78 names(plot_mat.melt)[2] <- "cols"
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79
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80 #if $adv.cluster:
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81
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82 plot_mat.dendo <- as.dendrogram(hclust(d = dist(x = subset(plot_mat, select = -rows))))
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83
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84 plot_mat.dendo.order <- order.dendrogram(plot_mat.dendo)
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85
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86 gg_rows = ggdendrogram(data = plot_mat.dendo, rotate = FALSE) +
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87 theme(axis.text.y = element_text(size = 6), axis.text.x = element_blank())
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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88
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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89 plot_mat.melt[,"rows"] <- factor(x = plot_mat.melt[,"rows"],
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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90 levels = unique(plot_mat.melt[,"rows"])[plot_mat.dendo.order],
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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91 ordered = TRUE)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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92
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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93 plot_mat.dendo <- as.dendrogram(hclust(d = dist(x = t(subset(plot_mat, select = -rows)))))
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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94 plot_mat.dendo.order <- order.dendrogram(plot_mat.dendo)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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95
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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96 gg_cols = ggdendrogram(data = plot_mat.dendo, rotate = TRUE) +
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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97 theme(axis.text.x = element_text(size = 6), axis.text.y = element_blank())
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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98
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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99 plot_mat.melt[,"cols"] <- factor(x = plot_mat.melt[,"cols"],
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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100 levels = unique(plot_mat.melt[,"cols"])[plot_mat.dendo.order],
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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101 ordered = TRUE)
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102
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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103 ## plot the heatmap
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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104 gg_hm = plot_mat.melt %>%
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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105 ggplot(aes(x = rows, y = cols, fill = value)) +
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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106 geom_tile() +
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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107 theme(legend.position = "bottom", axis.title.x = element_blank(), axis.title.y = element_blank(),
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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108 axis.text.x = element_text(angle = 90, hjust = 1)) +
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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109 colorscale
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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110
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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111 gg_empty = plot_mat.melt %>%
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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112 ggplot(aes(x = cols, y = value)) +
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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113 geom_blank() +
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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114 theme(axis.text = element_blank(),
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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115 axis.title = element_blank(),
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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116 line = element_blank(),
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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117 panel.background = element_blank())
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118
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119 plot_out <- ggarrange(
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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120 gg_rows, gg_empty, gg_hm, gg_cols,
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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121 nrow = 2, ncol = 2, widths = c(3, 1), heights = c(1, 3), newpage =F)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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122
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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123 #else
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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124
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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125 ## plot the heatmap
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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126 gg_hm = plot_mat.melt %>%
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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127 ggplot(aes(x = rows, y = cols, fill = value)) +
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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128 geom_tile() + ggtitle('$title') +
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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129 theme(legend.position = "bottom", axis.title.x = element_blank(), axis.title.y = element_blank(), axis.text.x = element_text(angle = 90, hjust = 1)) +
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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130 colorscale
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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131
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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132 plot_out <- gg_hm
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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133
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diff changeset
134 #end if
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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135
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
136 @SAVE_OUTPUT@
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
137 ]]></configfile>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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138 </configfiles>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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139 <inputs>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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140 <expand macro="read_complex_input"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
141 <expand macro="title"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
142 <!-- Advanced Options -->
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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143 <section name="adv" title="Advanced Options" expanded="false">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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144 <expand macro="transform" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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145 <param name="cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable data clustering" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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146 <param name="colorscheme" type="select" label="Heatmap colorscheme" >
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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147 <option value="whrd" selected="true">White to red</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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148 <option value="whblu">White to blue</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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149 <option value="blwhre">Blue to white to red</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
150 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
151 </section>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
152 <!-- Output Options -->
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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153 <section name="out" title="Output Options" expanded="true">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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154 <expand macro="dimensions" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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155 </section>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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156 </inputs>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
157 <outputs>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
158 <expand macro="additional_output" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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159 </outputs>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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160 <tests>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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161 <test>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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162 <param name="input1" value="mtcars.txt" ftype="tabular"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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163 <conditional name="inputdata">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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164 <param name="input_type" value="with_header_rownames"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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165 <param name="header" value="TRUE"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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166 <param name="row_names_index" value="1"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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167 <param name="sample_name_orientation" value="TRUE"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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168 </conditional>
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169 <param name="transform" value="log10plus1"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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170 <param name="cluster" value="true"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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171 <param name="colorscheme" value="blwhre"/>
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172 <param name="additional_output_format" value="pdf"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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173 <output name="output2" file="ggplot_heatmap_result1.pdf" compare="sim_size"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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174 </test>
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175 </tests>
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176 <help><![CDATA[
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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.
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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178
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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.
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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180 ]]></help>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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181 <citations>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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182 </citations>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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183 </tool>