diff test-data/expressionplot.txt @ 0:962b0ae5939f draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expressionplot.txt	Thu Jun 07 15:14:47 2018 -0400
@@ -0,0 +1,309 @@
+> 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
+> devname = dev.off()
+>