Mercurial > repos > dereeper > mlmm
comparison source_library/plot_MLMM.Ago.r @ 1:380b364980f9 draft default tip
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author | dereeper |
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date | Mon, 16 Apr 2018 08:50:05 -0400 |
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0:6b7107812931 | 1:380b364980f9 |
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1 ## fonction ########################################################################### | |
2 plot_MLMM.Ago<-function(x) { | |
3 output1 <-x$out[order(x$out$Pos),] | |
4 output_ok<-output1[order(output1$Chr),] | |
5 | |
6 maxpos<-c(0,cumsum(as.numeric(aggregate(output_ok$Pos,list(output_ok$Chr),max)$x+max(cumsum(as.numeric(aggregate(output_ok$Pos,list(output_ok$Chr),max)$x)))/200))) | |
7 plot_col<-rep(c('gray10','gray60'),ceiling(max(unique(output_ok$Chr))/2)) | |
8 # plot_col<-c('blue','darkgreen','red','cyan','purple') | |
9 size<-aggregate(output_ok$Pos,list(output_ok$Chr),length)$x | |
10 a<-rep(maxpos[1],size[1]) | |
11 b<-rep(plot_col[1],size[1]) | |
12 for (i in 2:max(unique(output_ok$Chr))){ | |
13 a<-c(a,rep(maxpos[i],size[i])) | |
14 b<-c(b,rep(plot_col[i],size[i]))} | |
15 | |
16 output_ok$xpos<-output_ok$Pos+a | |
17 output_ok$col<-b | |
18 output_ok$col[output_ok$mk=='qtl']<-'cyan' | |
19 output_ok$col[output_ok$SNP %in% x$cof]<-'red' | |
20 | |
21 d<-(aggregate(output_ok$xpos,list(output_ok$Chr),min)$x+aggregate(output_ok$xpos,list(output_ok$Chr),max)$x)/2 | |
22 | |
23 plot(output_ok$xpos,-log10(output_ok$pval),col=output_ok$col,pch=20,ylab='-log10(pval)',xaxt='n',xlab='chromosome') | |
24 axis(1,tick=FALSE,at=d,labels=c(1:max(unique(output_ok$Chr)))) | |
25 xline(output_ok$xpos[output_ok$mk=='qtl'], col='cyan', lwd=0.1) | |
26 abline(h=x$bonf_thresh,lty=3,col='black') | |
27 | |
28 | |
29 if (length(output_ok$pval[-log10(output_ok$pval) > x$bonf_thresh]) > 0) { | |
30 text(output_ok$xpos[-log10(output_ok$pval) > x$bonf_thresh], -log10(output_ok$pval[-log10(output_ok$pval) > x$bonf_thresh]), output_ok$SNP[-log10(output_ok$pval) > x$bonf_thresh], pos=3, cex=0.7) | |
31 legend("topright", lty=3, paste("bonf thresh :", x$bonf_thresh ,sep=" ")) | |
32 } else { | |
33 legend("topright", lty=3, paste("bonf thresh :", x$bonf_thresh ,sep=" ")) | |
34 } | |
35 | |
36 } |