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0
|
1
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2 caloffset = function(genome){
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3 total_len = sum(as.numeric(genome[,2]))
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4 offset = 0
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5 for (i in 1:nrow(genome)) {
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6 offset = c(offset,offset[i]+genome[i,2])
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7 }
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8 offset
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9 }
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10
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11 coverage = function(intervals,genome,offset,resolution) {
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12
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13 nChr = length(offset) - 1
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14 total_len = offset[nChr+1]
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15 nbin = as.integer(total_len / resolution)
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16
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17 pos = numeric(0)
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18 cov = numeric(0)#coverage
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19 col = numeric(0)#color
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20 for (i in 1:nChr) {
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21 d = x[x[,1]==as.character(genome[i,1]),2:3]
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22 d = ceiling(((d[,1]+d[,2])/2+offset[i])*nbin/total_len)
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23 t = table(d)
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24 pos = c(pos,as.numeric(row.names(t)))
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25 cov = c(cov, as.numeric(t))
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26 col = c(col,numeric(length(t))+i)
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27 }
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28 list(nbin=nbin,pos=pos,cov=cov,col=col)
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29 }
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30
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31 # plot coverage
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32 # res = genomeView(x,genome,100000)
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33 plotcov = function(res,genome,offset,title,uselog) {
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34 if (uselog == 'log'){
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35 res$cov = log10(res$cov+1)
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36 }
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37 ymax = max(res$cov)
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38 par(mar=c(5,5,5,1))
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39 plot(res$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$nbin),ylim=c(0,ymax))
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40 xticks = numeric(nrow(genome))
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41 for (i in 1:nrow(genome)){
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42 xticks[i] = (offset[i]+offset[i+1])/2*res$nbin/offset[length(offset)]
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43 }
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44 mtext(genome[,1],side=1,at=xticks,adj=1,las=2,col=seq(nrow(genome)))
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45 }
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