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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:25:47 -0400
parents 78fcfc04fcfe
children
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1 ## Feature Selection ##
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2 options(echo = TRUE)
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3 get_features <- function(my_genes, f = "gene") {
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4 if (f == "isoforms")
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5 return(isoforms(my_genes))
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6 else if (f == "tss")
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7 return(TSS(my_genes))
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8 else if (f == "cds")
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9 return(CDS(my_genes))
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10 else
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11 return(my_genes)
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12 }
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14 ## Main Function ##
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15
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16 library(argparse)
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17
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18 parser <- ArgumentParser(description = "Create a plot with cummeRbund")
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19
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20 parser$add_argument("--type", dest = "plotType", default = "Density", required = TRUE)
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21 parser$add_argument("--height", dest = "height", type = "integer", default = 960, required = TRUE)
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22 parser$add_argument("--width", dest = "width", type = "integer", default = 1280, required = TRUE)
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23 parser$add_argument("--outfile", dest = "filename", default = "plot-unknown-0.png", required = TRUE)
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24 parser$add_argument("--input", dest = "input_database", default = "cuffData.db", required = TRUE)
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25 parser$add_argument("--smooth", dest = "smooth", action = "store_true", default = FALSE)
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26 parser$add_argument("--gene_selector", dest = "gene_selector", action = "store_true", default = FALSE)
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27 parser$add_argument("--replicates", dest = "replicates", action = "store_true", default = FALSE)
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28 parser$add_argument("--labcol", dest = "labcol", action = "store_true", default = FALSE)
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29 parser$add_argument("--labrow", dest = "labrow", action = "store_true", default = FALSE)
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30 parser$add_argument("--border", dest = "border", action = "store_true", default = FALSE)
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31 parser$add_argument("--summary", dest = "summary", action = "store_true", default = FALSE)
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32 parser$add_argument("--count", dest = "count", action = "store_true", default = FALSE)
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33 parser$add_argument("--error_bars", dest = "error_bars", action = "store_true", default = FALSE)
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34 parser$add_argument("--log10", dest = "log10", action = "store_true", default = FALSE)
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35 parser$add_argument("--features", dest = "features", action = "store", default = "genes")
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36 parser$add_argument("--clustering", dest = "clustering", action = "store", default = "both")
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37 parser$add_argument("--iter_max", dest = "iter_max", action = "store")
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38 parser$add_argument("--genes", dest = "genes", action = "append")
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39 parser$add_argument("--k", dest = "k", action = "store")
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40 parser$add_argument("--x", dest = "x", action = "store")
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41 parser$add_argument("--y", dest = "y", action = "store")
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43 args <- parser$parse_args()
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44
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45 ## Load cummeRbund library
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46 library("cummeRbund")
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47
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48 ## Initialize cuff object
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49 cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
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50
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51 ## Print out info
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52 print(cuff)
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53 sink("cuffdb_info.txt")
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54 print(cuff)
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55 print("SAMPLES:")
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56 samples(cuff)
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57 print("REPLICATES:")
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58 replicates(cuff)
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59 print("FEATURES:")
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60 print(annotation(genes(cuff)))
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61 cat(annotation(genes(cuff))[[1]], sep = ",")
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62 sink()
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63
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64 png(filename = args$filename, width = args$width, height = args$height)
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65 tryCatch({
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66 if (args$plotType == "density") {
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67 csDensity(genes(cuff), replicates = args$replicates, logMode = args$log10)
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68 } else if (args$plotType == "boxplot") {
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69 csBoxplot(genes(cuff), replicates = args$replicates, logMode = args$log10)
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70 } else if (args$plotType == "mds") {
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71 MDSplot(genes(cuff), replicates = args$replicates)
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72 } else if (args$plotType == "pca") {
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73 PCAplot(genes(cuff), "PC1", "PC2", replicates = args$replicates)
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74 } else if (args$plotType == "dendrogram") {
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75 csDendro(genes(cuff), replicates = args$replicates)
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76 } else if (args$plotType == "scatter") {
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77 if (args$gene_selector) {
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78 my_genes <- get_features(getGenes(cuff, args$genes), args$features)
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79 } else {
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80 my_genes <- genes(cuff)
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81 }
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82 csScatter(my_genes, args$x, args$y, smooth = args$smooth, logMode = args$log10)
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83 } else if (args$plotType == "volcano") {
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84 if (args$gene_selector) {
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85 my_genes <- get_features(getGenes(cuff, args$genes), args$features)
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86 } else {
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87 my_genes <- genes(cuff)
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88 }
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89 csVolcano(my_genes, args$x, args$y)
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90 } else if (args$plotType == "heatmap") {
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91 if (args$gene_selector) {
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92 my_genes <- getGenes(cuff, args$genes)
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93 } else {
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94 my_genes <- getGenes(cuff, annotation(genes(cuff))[[1]])
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95 }
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96 csHeatmap(get_features(my_genes, args$features), clustering = args$clustering, labCol = args$labcol, labRow = args$labrow, border = args$border, logMode = args$log10)
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97 } else if (args$plotType == "cluster") {
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98 my_genes <- getGenes(cuff, args$genes)
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99 csCluster(get_features(my_genes, args$features), k = args$k)
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100 } else if (args$plotType == "dispersion") {
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101 dispersionPlot(genes(cuff))
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102 } else if (args$plotType == "fpkmSCV") {
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103 fpkmSCVPlot(genes(cuff))
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104 } else if (args$plotType == "scatterMatrix") {
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105 csScatterMatrix(genes(cuff))
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106 } else if (args$plotType == "expressionplot") {
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107 my_genes <- getGenes(cuff, args$genes)
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108 expressionPlot(get_features(my_genes, args$features), drawSummary = args$summary, showErrorbars = args$error_bars, replicates = args$replicates)
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109 } else if (args$plotType == "expressionbarplot") {
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110 my_gene_id <- args$genes
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111 my_genes <- getGenes(cuff, my_gene_id)
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112 expressionBarplot(get_features(my_genes, args$features), showErrorbars = args$error_bars, replicates = args$replicates)
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113 } else if (args$plotType == "mds") {
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114 MDSplot(genes(cuff), replicates = args$replicates)
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115 } else if (args$plotType == "pca") {
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116 PCAplot(genes(cuff), "PC1", "PC2", replicates = args$replicates)
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117 } else if (args$plotType == "maplot") {
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118 MAplot(genes(cuff), args$x, args$y, useCount = args$count)
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119 } else if (args$plotType == "genetrack") {
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120 my_gene <- getGene(cuff, args$genes)
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121 plotTracks(makeGeneRegionTrack(my_gene))
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122 }
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123 }, error = function(e) {
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124 write(paste("Failed:", e, sep = " "), stderr())
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125 q("no", 1, TRUE)
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126 })
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127 devname <- dev.off()
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128 print("cummeRbund finished")