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] "gene"

$filename
[1] "plot-heatmap-0.png"

$gene_selector
[1] FALSE

$genes
[1] "XLOC_000078"

$height
[1] 960

$input_database
[1] "/tmp/tmpCu9yWT/tmpPy7OpW/database/files/000/dataset_22.dat"

$iter_max
NULL

$k
NULL

$labcol
[1] TRUE

$labrow
[1] TRUE

$log10
[1] TRUE

$plotType
[1] "heatmap"

$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)
+ })
Getting gene information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting isoforms information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting CDS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting TSS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting promoter information:
	distData
Getting splicing information:
	distData
Getting relCDS information:
	distData
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Fontconfig error: Cannot load default config file
> devname = dev.off()
> 
> #end for
>