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11
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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 cov = numeric(nbin)#coverage
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17 col = numeric(nbin)#color
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18 for (i in 1:nChr) {
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19 d = x[x[,1]==as.character(genome[i,1]),2:3]
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20 d = ceiling(((d[,1]+d[,2])/2+offset[i])*nbin/total_len)
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21 t = table(d)
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22 pos = as.numeric(row.names(t))
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23 cov[pos] = cov[pos] + as.numeric(t)
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24 col[pos] = i
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25 }
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26 list(nbin=nbin,cov=cov,col=col)
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27 }
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28
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29 # plot coverage
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30 # res = genomeView(x,genome,100000)
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31 plotcov = function(res,genome,offset,title,uselog) {
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32 if (uselog == 'log'){
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33 res$cov = log10(res$cov+1)
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34 }
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35 ymax = max(res$cov)
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36 #print(ymax)
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37 par(mar=c(5,5,5,1))
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38 plot(seq(length(res$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))
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39 xticks = numeric(nrow(genome))
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40 for (i in 1:nrow(genome)){
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41 xticks[i] = (offset[i]+offset[i+1])/2*res$nbin/offset[length(offset)]
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42 }
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43 mtext(genome[,1],side=1,at=xticks,adj=1,las=2,col=seq(nrow(genome)))
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44 }
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45
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46 union_correlation = function(x,y){
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47 z = x>0 | y>0
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48 cor(x[z],y[z])
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49 }
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50
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51
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52 heatmap2 = function(x,scale,sym,margins,labRow,labCol){
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53 h = heatmap(x,scale=scale,sym=sym,margins=margins,labRow=labRow,labCol=labCol)
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54 x = x[h$rowInd,h$colInd]
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55 tx = numeric(0)
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56 ty = numeric(0)
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57 txt = character(0)
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58 for (i in 1:nrow(x)){
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59 for (j in 1:ncol(x)){
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60 tx <- c(tx,i)
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61 ty <- c(ty,ncol(x)-j+1)
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62 txt <- c(txt,format(x[i,j],digits=2,nsmall=2))
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63 }
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64 }
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65 #heatmap(x,scale=scale,sym=sym,margins=margins,labRow=labRow[h$rowInd],labCol=labCol[h$colInd],add.expr=text(1:4,1:4,1:4))
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66 cat(dim(tx))
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67 text(tx,ty,txt)
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68 heatmap(x,scale=scale,sym=sym,margins=margins,labRow=labRow[h$rowInd],labCol=labCol[h$colInd],add.expr=text(tx,ty,txt))
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69
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70 }
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