Nothing
CG_karyotype <- function(chr,start,end,int,ai,
name='',xlim=c(0,2.4),ylim=c(0.3,1))
{
png(paste(name,'_karyotype.png',sep=''),width=1300,height=1300)
#packagepath = system.file(package="patchwork")
#load(paste(packagepath,"/data/ideogram.RData",sep=""))
data(ideogram,package="patchworkCG")
#colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
#colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
colors_p <- colorRampPalette(c("#2754e8","#ad09e8"),space="rgb")
colors_q <- colorRampPalette(c("#c309e8","#e81e2c"),space="rgb")
layout(matrix(1:25,nrow=5,byrow=T), widths=1,heights=1)
aix=ai!=0
chr=chr[aix]
start=start[aix]
end=end[aix]
int=int[aix]
ai=ai[aix]
pos <- (start+end)/2
length=end-start
size=rep(0.5,length(chr))
size[length>1000000]=0.5
size[length>3000000]=1
size[length>5000000]=1.5
size[length>10000000]=2
size[length>20000000]=2.5
for (c in 1:24)
{
this <- ideogram[ideogram$c==c,]
ix <- chr==this$chr
ix[is.na(ix)]=FALSE
ix_p = ix & (pos < this$start)
ix_q = ix & (pos > this$end)
col <- rep('#B0B0B070',length(chr))
#loc = list of colors
loc_p=colors_p(ceiling(this$start/100))
loc_q=colors_q(ceiling((this$length - this$end)/100))
col[ix_p] = paste(loc_p[ceiling(pos[ix_p]/100)],'70',sep='')
col[ix_q] = paste(loc_q[ceiling((pos[ix_q]-this$end)/100)],'70',sep='')
plot(c(int[!ix],int[ix]),c(ai[!ix],ai[ix]),
pch=16,
cex=c(size[!ix],size[ix]),
cex.lab=3,
mar=c(0.1,0.1,0.1,0.1),
main = "",
xlab = this$chr,
ylab = "",
col = c(col[!ix],col[ix]),
xlim = xlim,
ylim = ylim,
yaxt="n",
xaxt="n")
axis(1,cex.axis=1.5)
axis(2,cex.axis=1.5)
par(new=F)
}
dev.off()
}
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