comparison tools/mytools/genomeview_notused @ 0:9071e359b9a3

Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1
2 caloffset = function(genome){
3 total_len = sum(as.numeric(genome[,2]))
4 offset = 0
5 for (i in 1:nrow(genome)) {
6 offset = c(offset,offset[i]+genome[i,2])
7 }
8 offset
9 }
10
11 coverage = function(intervals,genome,offset,resolution) {
12
13 nChr = length(offset) - 1
14 total_len = offset[nChr+1]
15 nbin = as.integer(total_len / resolution)
16
17 pos = numeric(0)
18 cov = numeric(0)#coverage
19 col = numeric(0)#color
20 for (i in 1:nChr) {
21 d = x[x[,1]==as.character(genome[i,1]),2:3]
22 d = ceiling(((d[,1]+d[,2])/2+offset[i])*nbin/total_len)
23 t = table(d)
24 pos = c(pos,as.numeric(row.names(t)))
25 cov = c(cov, as.numeric(t))
26 col = c(col,numeric(length(t))+i)
27 }
28 list(nbin=nbin,pos=pos,cov=cov,col=col)
29 }
30
31 # plot coverage
32 # res = genomeView(x,genome,100000)
33 plotcov = function(res,genome,offset,title,uselog) {
34 if (uselog == 'log'){
35 res$cov = log10(res$cov+1)
36 }
37 ymax = max(res$cov)
38 par(mar=c(5,5,5,1))
39 plot(res$pos,res$cov,type='h',cex=0.1,cex.axis=2,cex.lab=2,cex.main=3,col=res$col,xaxt='n',main=title,xlab='chromosome',ylab='coverage',frame.plot=F,xlim=c(0,res$nbin),ylim=c(0,ymax))
40 xticks = numeric(nrow(genome))
41 for (i in 1:nrow(genome)){
42 xticks[i] = (offset[i]+offset[i+1])/2*res$nbin/offset[length(offset)]
43 }
44 mtext(genome[,1],side=1,at=xticks,adj=1,las=2,col=seq(nrow(genome)))
45 }