Mercurial > repos > xuebing > sharplabtool
comparison mytools/genomeview.r @ 7:f0dc65e7f6c0
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:59:07 -0500 |
| parents | |
| children |
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| 6:094f377db4e5 | 7:f0dc65e7f6c0 |
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| 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 cov = numeric(nbin)#coverage | |
| 17 col = numeric(nbin)#color | |
| 18 for (i in 1:nChr) { | |
| 19 d = x[x[,1]==as.character(genome[i,1]),2:3] | |
| 20 d = ceiling(((d[,1]+d[,2])/2+offset[i])*nbin/total_len) | |
| 21 t = table(d) | |
| 22 pos = as.numeric(row.names(t)) | |
| 23 cov[pos] = cov[pos] + as.numeric(t) | |
| 24 col[pos] = i | |
| 25 } | |
| 26 list(nbin=nbin,cov=cov,col=col) | |
| 27 } | |
| 28 | |
| 29 # plot coverage | |
| 30 # res = genomeView(x,genome,100000) | |
| 31 plotcov = function(res,genome,offset,title,uselog) { | |
| 32 if (uselog == 'log'){ | |
| 33 res$cov = log10(res$cov+1) | |
| 34 } | |
| 35 ymax = max(res$cov) | |
| 36 #print(ymax) | |
| 37 par(mar=c(5,5,5,1)) | |
| 38 plot(seq(length(res$cov)),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,ylim=c(0,ymax)) | |
| 39 xticks = numeric(nrow(genome)) | |
| 40 for (i in 1:nrow(genome)){ | |
| 41 xticks[i] = (offset[i]+offset[i+1])/2*res$nbin/offset[length(offset)] | |
| 42 } | |
| 43 mtext(genome[,1],side=1,at=xticks,adj=1,las=2,col=seq(nrow(genome))) | |
| 44 } | |
| 45 | |
| 46 union_correlation = function(x,y){ | |
| 47 z = x>0 | y>0 | |
| 48 cor(x[z],y[z]) | |
| 49 } | |
| 50 | |
| 51 | |
| 52 heatmap2 = function(x,scale,sym,margins,labRow,labCol){ | |
| 53 h = heatmap(x,scale=scale,sym=sym,margins=margins,labRow=labRow,labCol=labCol) | |
| 54 x = x[h$rowInd,h$colInd] | |
| 55 tx = numeric(0) | |
| 56 ty = numeric(0) | |
| 57 txt = character(0) | |
| 58 for (i in 1:nrow(x)){ | |
| 59 for (j in 1:ncol(x)){ | |
| 60 tx <- c(tx,i) | |
| 61 ty <- c(ty,ncol(x)-j+1) | |
| 62 txt <- c(txt,format(x[i,j],digits=2,nsmall=2)) | |
| 63 } | |
| 64 } | |
| 65 #heatmap(x,scale=scale,sym=sym,margins=margins,labRow=labRow[h$rowInd],labCol=labCol[h$colInd],add.expr=text(1:4,1:4,1:4)) | |
| 66 cat(dim(tx)) | |
| 67 text(tx,ty,txt) | |
| 68 heatmap(x,scale=scale,sym=sym,margins=margins,labRow=labRow[h$rowInd],labCol=labCol[h$colInd],add.expr=text(tx,ty,txt)) | |
| 69 | |
| 70 } |