Mercurial > repos > nilesh > rseqc
diff test-data/output2.geneBodyCoverage.r @ 50:f242ee103277 draft
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
author | lparsons |
---|---|
date | Tue, 03 May 2016 16:36:57 -0400 |
parents | 6b33e31bda10 |
children | 09846d5169fa |
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--- a/test-data/output2.geneBodyCoverage.r Thu Jul 16 17:43:43 2015 -0400 +++ b/test-data/output2.geneBodyCoverage.r Tue May 03 16:36:57 2016 -0400 @@ -1,8 +1,21 @@ d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam <- c(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0) +d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam <- c(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0) +d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam <- c(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0) +data_matrix <- matrix(c(d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam), byrow=T, ncol=100) +rowLabel <- c("d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam","d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam","d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam") + + +pdf("output.geneBodyCoverage.heatMap.pdf") +rc <- cm.colors(ncol(data_matrix)) +heatmap(data_matrix, scale=c("none"),keep.dendro=F, labRow = rowLabel ,Colv = NA,Rowv = NA,labCol=NA,col=cm.colors(256),margins = c(6, 8),ColSideColors = rc,cexRow=1,cexCol=1,xlab="Gene body percentile (5'->3')", add.expr=x_axis_expr <- axis(side=1,at=c(1,10,20,30,40,50,60,70,80,90,100),labels=c("1","10","20","30","40","50","60","70","80","90","100"))) +dev.off() pdf("output.geneBodyCoverage.curves.pdf") x=1:100 -icolor = colorRampPalette(c("#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"))(1) +icolor = colorRampPalette(c("#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"))(3) plot(x,d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,type='l',xlab="Gene body percentile (5'->3')", ylab="Coverage",lwd=0.8,col=icolor[1]) +lines(x,d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,type='l',col=icolor[2]) +lines(x,d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,type='l',col=icolor[3]) +legend(0,1,fill=icolor[1:3], legend=c('d1_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam','d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam','d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam')) dev.off()