cummerbund: cummeRbund.R annotate

annotate cummeRbund.R @ 5:78fcfc04fcfe draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3

author	devteam
date	Thu, 23 Feb 2017 20:24:03 -0500
parents	587c425b4e76
children	c3b54a4b7741

rev	line source
0 587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	1 ## Feature Selection ##
5 78fcfc04fcfe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	2 options(echo=TRUE)
0 587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	3 get_features <- function(myGenes, f="gene") {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	4 if (f == "isoforms")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	5 return(isoforms(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	6 else if (f == "tss")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	7 return(TSS(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	8 else if (f == "cds")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	9 return(CDS(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	10 else
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	11 return(myGenes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	12 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	13
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	14 ## Main Function ##
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	15
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	16 library(argparse)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	17
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	18 parser <- ArgumentParser(description='Create a plot with cummeRbund')
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	19
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	20 parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	21 parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	22 parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	23 parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	24 parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	25 parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	26 parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	27 parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	28 parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	29 parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	30 parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	31 parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	32 parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	33 parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	34 parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	35 parser$add_argument('--features', dest='features', action="store", default="genes")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	36 parser$add_argument('--clustering', dest='clustering', action="store", default="both")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	37 parser$add_argument('--iter_max', dest='iter_max', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	38 parser$add_argument('--genes', dest='genes', action="append")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	39 parser$add_argument('--k', dest='k', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	40 parser$add_argument('--x', dest='x', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	41 parser$add_argument('--y', dest='y', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	42
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	43 args <- parser$parse_args()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	44
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	45 ## Load cummeRbund library
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	46 library("cummeRbund")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	47
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	48 ## Initialize cuff object
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	49 cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	50
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	51 ## Print out info
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	52 print(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	53 sink("cuffdb_info.txt")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	54 print(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	55 print("SAMPLES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	56 samples(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	57 print("REPLICATES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	58 replicates(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	59 print("FEATURES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	60 print(annotation(genes(cuff)))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	61 cat(annotation(genes(cuff))[[1]],sep=",")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	62 sink()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	63
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	64 png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	65 tryCatch({
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	66 if (args$plotType == 'density') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	67 csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	68 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	69 else if (args$plotType == 'boxplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	70 csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	71 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	72 else if (args$plotType == 'mds') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	73 MDSplot(genes(cuff), replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	74 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	75 else if (args$plotType == 'pca') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	76 PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	77 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	78 else if (args$plotType == 'dendrogram') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	79 csDendro(genes(cuff), replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	80 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	81 else if (args$plotType == 'scatter') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	82 if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	83 myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	84 csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	85 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	86 else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	87 csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	88 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	89 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	90 else if (args$plotType == 'volcano') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	91 if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	92 myGenes <- get_features(getGenes(cuff, args$genes), args$features)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	93 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	94 else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	95 myGenes <- genes(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	96 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	97 csVolcano(myGenes, args$x, args$y)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	98 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	99 else if (args$plotType == 'heatmap') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	100 if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	101 myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	102 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	103 else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	104 myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	105 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	106 csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	107 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	108 else if (args$plotType == 'cluster') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	109 myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	110 csCluster(get_features(myGenes, args$features), k=args$k)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	111 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	112 else if (args$plotType == 'dispersion') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	113 dispersionPlot(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	114 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	115 else if (args$plotType == 'fpkmSCV') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	116 fpkmSCVPlot(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	117 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	118 else if (args$plotType == 'scatterMatrix') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	119 csScatterMatrix(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	120 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	121 else if (args$plotType == 'expressionplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	122 myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	123 expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	124 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	125 else if (args$plotType == 'expressionbarplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	126 myGeneId <- args$genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	127 myGenes <- getGenes(cuff, myGeneId)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	128 expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	129 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	130 else if (args$plotType == 'mds') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	131 MDSplot(genes(cuff),replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	132 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	133 else if (args$plotType == 'pca') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	134 PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	135 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	136 else if (args$plotType == 'maplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	137 MAplot(genes(cuff), args$x, args$y, useCount=args$count)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	138 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	139 else if (args$plotType == 'genetrack') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	140 myGene <- getGene(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	141 plotTracks(makeGeneRegionTrack(myGene))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	142 }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	143 },error = function(e) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	144 write(paste("Failed:", e, sep=" "), stderr())
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	145 q("no", 1, TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	146 })
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	147 devname = dev.off()

Mercurial > repos > devteam > cummerbund

annotate cummeRbund.R @ 5:78fcfc04fcfe draft