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comparison 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
parents
children aefbcaf15a94
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-1:000000000000 0:e462121e8269
1 ## Feature Selection ##
2 get_features <- function(myGenes, f="gene") {
3 if (f == "isoforms")
4 return(isoforms(myGenes))
5 else if (f == "tss")
6 return(TSS(myGenes))
7 else if (f == "cds")
8 return(CDS(myGenes))
9 else
10 return(myGenes)
11 }
12
13 ## Main Function ##
14
15 library(argparse)
16
17 parser <- ArgumentParser(description='Create a plot with cummeRbund')
18
19 parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
20 parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
21 parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
22 parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
23 parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
24 parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
25 parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
26 parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
27 parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
28 parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
29 parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
30 parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
31 parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
32 parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
33 parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
34 parser$add_argument('--features', dest='features', action="store", default="genes")
35 parser$add_argument('--clustering', dest='clustering', action="store", default="both")
36 parser$add_argument('--iter_max', dest='iter_max', action="store")
37 parser$add_argument('--genes', dest='genes', action="append")
38 parser$add_argument('--k', dest='k', action="store")
39 parser$add_argument('--x', dest='x', action="store")
40 parser$add_argument('--y', dest='y', action="store")
41
42 args <- parser$parse_args()
43
44 ## Load cummeRbund library
45 library("cummeRbund")
46
47 ## Initialize cuff object
48 cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
49
50 ## Print out info
51 print(cuff)
52 sink("cuffdb_info.txt")
53 print(cuff)
54 print("SAMPLES:")
55 samples(cuff)
56 print("REPLICATES:")
57 replicates(cuff)
58 print("FEATURES:")
59 print(annotation(genes(cuff)))
60 cat(annotation(genes(cuff))[[1]],sep=",")
61 sink()
62
63 png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
64 tryCatch({
65 if (args$plotType == 'density') {
66 csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
67 }
68 else if (args$plotType == 'boxplot') {
69 csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
70 }
71 else if (args$plotType == 'mds') {
72 MDSplot(genes(cuff), replicates=args$replicates)
73 }
74 else if (args$plotType == 'pca') {
75 PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
76 }
77 else if (args$plotType == 'dendrogram') {
78 csDendro(genes(cuff), replicates=args$replicates)
79 }
80 else if (args$plotType == 'scatter') {
81 if (args$gene_selector) {
82 myGenes <- getGenes(cuff, args$genes)
83 csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
84 }
85 else {
86 csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
87 }
88 }
89 else if (args$plotType == 'volcano') {
90 if (args$gene_selector) {
91 myGenes <- get_features(getGenes(cuff, args$genes), args$features)
92 }
93 else {
94 myGenes <- genes(cuff)
95 }
96 csVolcano(myGenes, args$x, args$y)
97 }
98 else if (args$plotType == 'heatmap') {
99 if (args$gene_selector) {
100 myGenes <- getGenes(cuff, args$genes)
101 }
102 else {
103 myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
104 }
105 csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)
106 }
107 else if (args$plotType == 'cluster') {
108 myGenes <- getGenes(cuff, args$genes)
109 csCluster(get_features(myGenes, args$features), k=args$k)
110 }
111 else if (args$plotType == 'dispersion') {
112 dispersionPlot(genes(cuff))
113 }
114 else if (args$plotType == 'fpkmSCV') {
115 fpkmSCVPlot(genes(cuff))
116 }
117 else if (args$plotType == 'scatterMatrix') {
118 csScatterMatrix(genes(cuff))
119 }
120 else if (args$plotType == 'expressionplot') {
121 myGenes <- getGenes(cuff, args$genes)
122 expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
123 }
124 else if (args$plotType == 'expressionbarplot') {
125 myGeneId <- args$genes
126 myGenes <- getGenes(cuff, myGeneId)
127 expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
128 }
129 else if (args$plotType == 'mds') {
130 MDSplot(genes(cuff),replicates=args$replicates)
131 }
132 else if (args$plotType == 'pca') {
133 PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
134 }
135 else if (args$plotType == 'maplot') {
136 MAplot(genes(cuff), args$x, args$y, useCount=args$count)
137 }
138 else if (args$plotType == 'genetrack') {
139 myGene <- getGene(cuff, args$genes)
140 plotTracks(makeGeneRegionTrack(myGene))
141 }
142 },error = function(e) {
143 write(paste("Failed:", e, sep=" "), stderr())
144 q("no", 1, TRUE)
145 })
146 devname = dev.off()