Mercurial > repos > iuc > ggplot2_heatmap

annotate ggplot2_heatmap.xml @ 0:f44dc95928aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
author iuc
date Mon, 11 Jun 2018 16:04:51 -0400
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children 391a4cc45fea
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f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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1 <tool id="ggplot2_heatmap" name="Heatmap w ggplot" version="@VERSION@">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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2 <macros>
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3 <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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4 </macros>
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5 <requirements>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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6 <requirement type="package" version="0.9.2">r-cowplot</requirement>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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7 <requirement type="package" version="0.2.0">r-egg</requirement>
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8 <requirement type="package" version="0.1_20">r-ggdendro</requirement>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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9 <requirement type="package" version="0.7.4">r-dplyr</requirement>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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10 <requirement type="package" version="1.4.3">r-reshape2</requirement>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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11 <requirement type="package" version="1.2.1">r-svglite</requirement>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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12 </requirements>
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13 <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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14 cat '$script' &&
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15 Rscript '$script'
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16 ]]></command>
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17 <configfiles>
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18 <configfile name="script"><![CDATA[
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19 @R_INIT@
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20
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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21 ## Import library
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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22
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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23 library(ggplot2)
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24 library(cowplot)
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25 library(egg)
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26 library(dplyr)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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27 library(ggdendro)
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28 library(reshape2)
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29
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30 input <- '$input1'
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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31 header <- ${inputdata.header}
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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32 rowname_index <- as.integer('$inputdata.row_names_index')
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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33
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34 transform <- '$adv.transform'
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35
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36 ## read table with or with out header or row_names
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37 if(rowname_index > 0){
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38 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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39 }else{
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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40 df <- read.table(input, header = header, sep = "\t")
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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41 }
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42
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43 hclust_fun = function(x) hclust(x, method="complete")
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44 dist_fun = function(x) dist(x, method="maximum")
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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45 distfun=dist_fun
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46 hclustfun=hclust_fun
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47
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48 plot_mat <- df
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49
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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50 ## transform dataset
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51 if(transform == "log2"){
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52 plot_mat <- log2(plot_mat)
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53 cat("\n ", transform, " transformed")
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54 }else if(transform == "log2plus1"){
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55 plot_mat <- log2(plot_mat+1)
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56 cat("\n ", transform, " transformed")
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57 }else if(transform == "log10"){
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58 plot_mat <- log10(plot_mat)
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59 cat("\n ", transform, " transformed")
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60 }else if(transform == "log10plus1"){
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61 plot_mat <- log10(plot_mat+1)
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62 cat("\n ", transform, " transformed")
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63 }else{
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64 plot_mat <- plot_mat
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65 }
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66
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67 #if $adv.colorscheme == "whrd"
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68 colorscale = scale_fill_gradient(low="white", high="red", guide="colorbar")
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69 #elif $adv.colorscheme == "whblu"
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70 colorscale = scale_fill_gradient(low="white", high="blue", guide="colorbar")
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71 #elif $adv.colorscheme == "blwhre"
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72 colorscale = scale_fill_gradient2(low="blue", mid="white", high="red", guide="colorbar")
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73 #end if
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74
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75 plot_mat["rows"] <- row.names(plot_mat)
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76 plot_mat.melt <- melt(plot_mat, id.vars = "rows")
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77 names(plot_mat.melt)[2] <- "cols"
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78
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79 #if $adv.cluster:
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81 plot_mat.dendo <- as.dendrogram(hclust(d = dist(x = subset(plot_mat, select = -rows))))
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82
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83 plot_mat.dendo.order <- order.dendrogram(plot_mat.dendo)
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84
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85 gg_rows = ggdendrogram(data = plot_mat.dendo, rotate = FALSE) +
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86 theme(axis.text.y = element_text(size = 6), axis.text.x = element_blank())
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87
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88 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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89 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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90 ordered = TRUE)
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91
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92 plot_mat.dendo <- as.dendrogram(hclust(d = dist(x = t(subset(plot_mat, select = -rows)))))
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93 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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94
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95 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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96 theme(axis.text.x = element_text(size = 6), axis.text.y = element_blank())
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97
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98 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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99 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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100 ordered = TRUE)
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101
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102 ## plot the heatmap
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103 gg_hm = plot_mat.melt %>%
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104 ggplot(aes(x = rows, y = cols, fill = value)) +
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105 geom_tile() +
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106 theme(legend.position = "bottom", axis.title.x = element_blank(), axis.title.y = element_blank(),
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107 axis.text.x = element_text(angle = 90, hjust = 1)) +
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108 colorscale
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109
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110 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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111 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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112 geom_blank() +
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113 theme(axis.text = element_blank(),
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114 axis.title = element_blank(),
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115 line = element_blank(),
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116 panel.background = element_blank())
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117
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118 plot_out <- ggarrange(
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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119 gg_rows, gg_empty, gg_hm, gg_cols,
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120 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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121
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122 #else
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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123
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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124 ## plot the heatmap
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125 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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126 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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127 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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128 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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129 colorscale
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130
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131 plot_out <- gg_hm
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132
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133 #end if
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134
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135 @SAVE_OUTPUT@
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136 ]]></configfile>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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137 </configfiles>
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138 <inputs>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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139 <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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140 <expand macro="title"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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141 <!-- Advanced Options -->
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142 <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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143 <expand macro="transform" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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144 <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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145 <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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146 <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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147 <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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148 <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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149 </param>
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150 </section>
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151 <!-- Output Options -->
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152 <section name="out" title="Output Options" expanded="true">
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153 <expand macro="dimensions" />
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154 </section>
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155 </inputs>
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156 <outputs>
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157 <expand macro="additional_output" />
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158 </outputs>
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159 <tests>
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160 <test>
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161 <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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162 <conditional name="inputdata">
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163 <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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164 <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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165 <param name="row_names_index" value="1"/>
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166 <param name="sample_name_orientation" value="TRUE"/>
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167 </conditional>
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168 <param name="transform" value="log10plus1"/>
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169 <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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170 <param name="colorscheme" value="blwhre"/>
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171 <param name="additional_output_format" value="pdf"/>
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172 <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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173 </test>
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174 </tests>
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175 <help><![CDATA[
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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176 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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177
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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178 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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179 ]]></help>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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180 <citations>
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 </tool>