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annotate cummeRbund.R @ 0:e462121e8269 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:27:38 -0500
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e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
1 ## Feature Selection ##
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 get_features <- function(myGenes, f="gene") {
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 if (f == "isoforms")
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4 return(isoforms(myGenes))
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5 else if (f == "tss")
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6 return(TSS(myGenes))
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7 else if (f == "cds")
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8 return(CDS(myGenes))
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9 else
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10 return(myGenes)
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11 }
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12
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13 ## Main Function ##
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14
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 library(argparse)
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16
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17 parser <- ArgumentParser(description='Create a plot with cummeRbund')
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18
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19 parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
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20 parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
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22 parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
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23 parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
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24 parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
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25 parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
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26 parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
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27 parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
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28 parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
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29 parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
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30 parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
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31 parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
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32 parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
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33 parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
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34 parser$add_argument('--features', dest='features', action="store", default="genes")
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35 parser$add_argument('--clustering', dest='clustering', action="store", default="both")
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36 parser$add_argument('--iter_max', dest='iter_max', action="store")
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37 parser$add_argument('--genes', dest='genes', action="append")
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38 parser$add_argument('--k', dest='k', action="store")
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39 parser$add_argument('--x', dest='x', action="store")
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40 parser$add_argument('--y', dest='y', action="store")
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41
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42 args <- parser$parse_args()
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43
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44 ## Load cummeRbund library
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45 library("cummeRbund")
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46
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47 ## Initialize cuff object
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48 cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
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49
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50 ## Print out info
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51 print(cuff)
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52 sink("cuffdb_info.txt")
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53 print(cuff)
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54 print("SAMPLES:")
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55 samples(cuff)
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56 print("REPLICATES:")
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57 replicates(cuff)
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58 print("FEATURES:")
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59 print(annotation(genes(cuff)))
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60 cat(annotation(genes(cuff))[[1]],sep=",")
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61 sink()
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62
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63 png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
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64 tryCatch({
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65 if (args$plotType == 'density') {
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66 csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
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67 }
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68 else if (args$plotType == 'boxplot') {
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69 csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
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70 }
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71 else if (args$plotType == 'mds') {
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72 MDSplot(genes(cuff), replicates=args$replicates)
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73 }
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74 else if (args$plotType == 'pca') {
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75 PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
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76 }
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77 else if (args$plotType == 'dendrogram') {
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78 csDendro(genes(cuff), replicates=args$replicates)
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79 }
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80 else if (args$plotType == 'scatter') {
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81 if (args$gene_selector) {
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82 myGenes <- getGenes(cuff, args$genes)
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83 csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
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84 }
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85 else {
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86 csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
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87 }
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88 }
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89 else if (args$plotType == 'volcano') {
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90 if (args$gene_selector) {
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91 myGenes <- get_features(getGenes(cuff, args$genes), args$features)
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92 }
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93 else {
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94 myGenes <- genes(cuff)
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95 }
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96 csVolcano(myGenes, args$x, args$y)
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97 }
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98 else if (args$plotType == 'heatmap') {
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99 if (args$gene_selector) {
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100 myGenes <- getGenes(cuff, args$genes)
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101 }
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102 else {
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103 myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
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104 }
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105 csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)
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106 }
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107 else if (args$plotType == 'cluster') {
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108 myGenes <- getGenes(cuff, args$genes)
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109 csCluster(get_features(myGenes, args$features), k=args$k)
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110 }
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111 else if (args$plotType == 'dispersion') {
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112 dispersionPlot(genes(cuff))
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113 }
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114 else if (args$plotType == 'fpkmSCV') {
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115 fpkmSCVPlot(genes(cuff))
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116 }
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117 else if (args$plotType == 'scatterMatrix') {
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118 csScatterMatrix(genes(cuff))
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119 }
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120 else if (args$plotType == 'expressionplot') {
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121 myGenes <- getGenes(cuff, args$genes)
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122 expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
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123 }
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124 else if (args$plotType == 'expressionbarplot') {
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125 myGeneId <- args$genes
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126 myGenes <- getGenes(cuff, myGeneId)
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127 expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
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128 }
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129 else if (args$plotType == 'mds') {
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130 MDSplot(genes(cuff),replicates=args$replicates)
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131 }
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132 else if (args$plotType == 'pca') {
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133 PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
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134 }
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135 else if (args$plotType == 'maplot') {
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136 MAplot(genes(cuff), args$x, args$y, useCount=args$count)
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137 }
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138 else if (args$plotType == 'genetrack') {
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139 myGene <- getGene(cuff, args$genes)
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140 plotTracks(makeGeneRegionTrack(myGene))
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141 }
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142 },error = function(e) {
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143 write(paste("Failed:", e, sep=" "), stderr())
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144 q("no", 1, TRUE)
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145 })
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146 devname = dev.off()