cummerbund: cummeRbund.R annotate

annotate cummeRbund.R @ 2:ac2ebc60ef5d draft

Uploaded corrected dynamic options

author	devteam
date	Mon, 16 Mar 2015 15:43:02 -0400
parents	587c425b4e76
children	78fcfc04fcfe

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

Mercurial > repos > devteam > cummerbund

annotate cummeRbund.R @ 2:ac2ebc60ef5d draft