--- a/test-data/heatmap.txt	Thu Feb 23 20:24:03 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,311 +0,0 @@
-> 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()
-> 
-> ## Load cummeRbund library
-> library("cummeRbund")
-Loading required package: BiocGenerics
-Loading required package: methods
-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 objects are masked from ‘package:stats’:
-
-    IQR, mad, xtabs
-
-The following objects are masked from ‘package:base’:
-
-    anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
-    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
-    is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
-    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
-    Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
-    unique, unsplit, which, which.max, which.min
-
-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: stats4
-Loading required package: S4Vectors
-
-Attaching package: ‘S4Vectors’
-
-The following objects are masked from ‘package:base’:
-
-    colMeans, colSums, expand.grid, rowMeans, rowSums
-
-Loading required package: IRanges
-Loading required package: GenomeInfoDb
-Loading required package: Gviz
-Loading required package: grid
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘ensembldb’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-Warning: namespace ‘AnnotationHub’ is not available and has been replaced
-by .GlobalEnv when processing object ‘plot.index’
-
-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
-> devname = dev.off()
->