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comparison test-data/output2.geneBodyCoverage.r @ 51:09846d5169fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
parents f242ee103277
children
comparison
equal deleted inserted replaced
50:f242ee103277 51:09846d5169fa
1 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) 1 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)
2 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) 2 pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.1 <- 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)
3 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) 3 pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.2 <- 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)
4 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) 4 data_matrix <- matrix(c(pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.1,pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.2), byrow=T, ncol=100)
5 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") 5 rowLabel <- c("pairend_strandspecific_51mer_hg19_chr1_1_100000_bam","pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.1","pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.2")
6 6
7 7
8 pdf("output.geneBodyCoverage.heatMap.pdf") 8 pdf("output.geneBodyCoverage.heatMap.pdf")
9 rc <- cm.colors(ncol(data_matrix)) 9 rc <- cm.colors(ncol(data_matrix))
10 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"))) 10 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")))
12 12
13 13
14 pdf("output.geneBodyCoverage.curves.pdf") 14 pdf("output.geneBodyCoverage.curves.pdf")
15 x=1:100 15 x=1:100
16 icolor = colorRampPalette(c("#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"))(3) 16 icolor = colorRampPalette(c("#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"))(3)
17 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]) 17 plot(x,pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,type='l',xlab="Gene body percentile (5'->3')", ylab="Coverage",lwd=0.8,col=icolor[1])
18 lines(x,d2_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,type='l',col=icolor[2]) 18 lines(x,pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.1,type='l',col=icolor[2])
19 lines(x,d3_pairend_strandspecific_51mer_hg19_chr1_1_100000_bam,type='l',col=icolor[3]) 19 lines(x,pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.2,type='l',col=icolor[3])
20 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')) 20 legend(0,1,fill=icolor[1:3], legend=c('pairend_strandspecific_51mer_hg19_chr1_1_100000_bam','pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.1','pairend_strandspecific_51mer_hg19_chr1_1_100000_bam.2'))
21 dev.off() 21 dev.off()