view test-data/maplot.txt @ 3:3a0ade59306a draft

Fixed help text.

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-maplot-0.png"

$gene_selector
[1] FALSE

$genes
NULL

$height
[1] 960

$input_database
[1] "/tmp/tmpk0xwrM/tmpNNuxXE/database/files/000/dataset_1.dat"

$iter_max
NULL

$k
NULL

$labcol
[1] FALSE

$labrow
[1] FALSE

$log10
[1] FALSE

$plotType
[1] "maplot"

$replicates
[1] FALSE

$smooth
[1] FALSE

$summary
[1] FALSE

$width
[1] 1280

$x
[1] "q1"

$y
[1] "q2"

> 
> #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
Warning message:
Removed 52 rows containing missing values (geom_point). 
> devname = dev.off()
> 
> #end for
>