Mercurial > repos > devteam > cummerbund
view test-data/dispersion.txt @ 0:587c425b4e76 draft
Initial commit with version 1.0.0 of the cummeRbund wrapper.
author | devteam |
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date | Tue, 23 Dec 2014 15:58:27 -0500 |
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children | 78fcfc04fcfe |
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R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) + else if (f == "tss") + return(TSS(myGenes)) + else if (f == "cds") + return(CDS(myGenes)) + else + return(myGenes) + } > > ## Main Function ## > > library(argparse) Loading required package: proto > > parser <- ArgumentParser(description='Create a plot with cummeRbund') > > parser$add_argument('--type', dest='plotType', default='Density', required=TRUE) > parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE) > parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE) > parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE) > parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE) > parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE) > parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE) > parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE) > parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE) > parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE) > parser$add_argument('--border', dest='border', action="store_true", default=FALSE) > parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE) > parser$add_argument('--count', dest='count', action="store_true", default=FALSE) > parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE) > parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE) > parser$add_argument('--features', dest='features', action="store", default="genes") > parser$add_argument('--clustering', dest='clustering', action="store", default="both") > parser$add_argument('--iter_max', dest='iter_max', action="store") > parser$add_argument('--genes', dest='genes', action="append") > parser$add_argument('--k', dest='k', action="store") > parser$add_argument('--x', dest='x', action="store") > parser$add_argument('--y', dest='y', action="store") > > args <- parser$parse_args() > > print(args) $border [1] FALSE $clustering [1] "both" $count [1] FALSE $error_bars [1] FALSE $features [1] "genes" $filename [1] "plot-dispersion-0.png" $gene_selector [1] FALSE $genes NULL $height [1] 960 $input_database [1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_25.dat" $iter_max NULL $k NULL $labcol [1] FALSE $labrow [1] FALSE $log10 [1] FALSE $plotType [1] "dispersion" $replicates [1] FALSE $smooth [1] FALSE $summary [1] FALSE $width [1] 1280 $x NULL $y NULL > > #q() > > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Loading required package: RSQLite Loading required package: DBI Loading required package: ggplot2 Loading required package: reshape2 Loading required package: fastcluster Attaching package: ‘fastcluster’ The following object is masked from ‘package:stats’: hclust Loading required package: rtracklayer Loading required package: GenomicRanges Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid Attaching package: ‘cummeRbund’ The following object is masked from ‘package:GenomicRanges’: promoters The following object is masked from ‘package:IRanges’: promoters The following object is masked from ‘package:BiocGenerics’: conditions > > ## Initialize cuff object > cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE) > > ## Print out info > print(cuff) CuffSet instance with: 2 samples 87 genes 90 isoforms 88 TSS 0 CDS 87 promoters 88 splicing 0 relCDS > sink("cuffdb_info.txt") > print(cuff) > print("SAMPLES:") > samples(cuff) > print("REPLICATES:") > replicates(cuff) > print("FEATURES:") > print(annotation(genes(cuff))) > cat(annotation(genes(cuff))[[1]],sep=",") > sink() > > png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png')) > tryCatch({ + if (args$plotType == 'density') { + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10) + } + else if (args$plotType == 'boxplot') { + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10) + } + else if (args$plotType == 'mds') { + MDSplot(genes(cuff), replicates=args$replicates) + } + else if (args$plotType == 'pca') { + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates) + } + else if (args$plotType == 'dendrogram') { + csDendro(genes(cuff), replicates=args$replicates) + } + else if (args$plotType == 'scatter') { + if (args$gene_selector) { + myGenes <- getGenes(cuff, args$genes) + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10) + } + else { + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10) + } + } + else if (args$plotType == 'volcano') { + if (args$gene_selector) { + myGenes <- get_features(getGenes(cuff, args$genes), args$features) + } + else { + myGenes <- genes(cuff) + } + csVolcano(myGenes, args$x, args$y) + } + else if (args$plotType == 'heatmap') { + if (args$gene_selector) { + myGenes <- getGenes(cuff, args$genes) + } + else { + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]]) + } + csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10) + } + else if (args$plotType == 'cluster') { + myGenes <- getGenes(cuff, args$genes) + csCluster(get_features(myGenes, args$features), k=args$k) + } + else if (args$plotType == 'dispersion') { + dispersionPlot(genes(cuff)) + } + else if (args$plotType == 'fpkmSCV') { + fpkmSCVPlot(genes(cuff)) + } + else if (args$plotType == 'scatterMatrix') { + csScatterMatrix(genes(cuff)) + } + else if (args$plotType == 'expressionplot') { + myGenes <- getGenes(cuff, args$genes) + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates) + } + else if (args$plotType == 'expressionbarplot') { + myGeneId <- args$genes + myGenes <- getGenes(cuff, myGeneId) + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates) + } + else if (args$plotType == 'mds') { + MDSplot(genes(cuff),replicates=args$replicates) + } + else if (args$plotType == 'pca') { + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates) + } + else if (args$plotType == 'maplot') { + MAplot(genes(cuff), args$x, args$y, useCount=args$count) + } + else if (args$plotType == 'genetrack') { + myGene <- getGene(cuff, args$genes) + plotTracks(makeGeneRegionTrack(myGene)) + } + },error = function(e) { + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) Fontconfig error: Cannot load default config file > devname = dev.off() > > #end for >