Nothing
CG_KaChCN <- function(chr,start,end,int,ai,Cn,mCn,mchr,mpos,mval,
sval,schr,spos,name='',xlim=c(0,2.4),ylim=c(0,1),maxCn=8)
{
#packagepath = system.file(package="patchwork")
#load(paste(packagepath,"/data/ideogram.RData",sep=""))
data(ideogram,package="patchworkCG")
#Origional
colors_p <- colorRampPalette(c("#2754e8","#ad09e8"),space="rgb")
colors_q <- colorRampPalette(c("#c309e8","#e81e2c"),space="rgb")
#colors_chrom = colorRampPalette(c("#6600FF","#CC0000"),space="rgb")
ai[is.na(ai)]=0
aix=ai!=0
chr=chr[aix]
start=start[aix]
end=end[aix]
int=int[aix]
ai=ai[aix]
Cn=Cn[aix]
mCn=mCn[aix]
pos <- (start+end)/2
length=end-start
size=rep(1,length(chr))
size[length>1000000]=2
size[length>3000000]=3
size[length>5000000]=4
size[length>10000000]=5
size[length>20000000]=6
for (c in 1:24)
{
this <- ideogram[ideogram$c==c,]
png(paste(name,'_KaChCN_',this$chr,'.png',sep=''),width=1080,height=1300)
layout(matrix(1:4,nrow=4,byrow=T), widths=10,heights=c(10,5,5,5))
mar.default <- c(5,4,4,2) + 0.1
par(mar = mar.default + c(0, 4, 0, 0))
#Create a list of colors length of chromosome.
#Assign color by middle of segment. (pos as an int).
ix <- chr==this$chr
ix_p = ix & (pos < this$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$end)/100)],'70',sep='')
#Origional
#col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
#col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
plot(c(int[!ix],int[ix]),c(ai[!ix],ai[ix]),
pch=16,
cex=c(size[!ix],size[ix]),
cex.lab=3,
#mar=c(0.1,0.1,0.1,0.1),
main = "",
xlab = "",
#ylab = "Allelic imbalance -->",
ylab = '',
col = c(col[!ix],col[ix]),
xlim = xlim,
ylim = ylim,
yaxt="n",
xaxt="n")
axis(1,at=seq(0,2.5,0.1),cex.axis=2)
axis(2,at=seq(0,1,0.1),cex.axis=2)
mtext(text="Allelic imbalance",side=2,line=4,las=3,cex=2)
mtext(text="Coverage, all segments",side=1,line=4,cex=2,las=1)
col=rep('#000000',sum(ix))
col[pos[ix] < this$mid] <- loc_p[ceiling(pos[ix][pos[ix] < this$mid]/100)]
col[pos[ix] > this$mid] <- loc_q[ceiling((pos[ix][pos[ix] > this$mid] - this$mid)/100)]
par(new=F)
plot(1,1,type='n',
xlab="",
ylab='',
cex.lab=3,
xlim = c(0,this$length),
ylim = c(-0.1,8.1),
yaxt="n",
xaxt="n")
axis(1,cex.axis=2)
axis(2,cex.axis=2)
mtext(text=paste('Total and minor copy number', this$chr),side=1,line=4,cex=2,las=1)
segments(x0=start[ix],x1=end[ix],
y0=Cn[ix],y1=Cn[ix],
col=col,
lwd=5,) #Om fel, prova ta bort detta komma
segments(x0=start[ix],x1=end[ix],
y0=mCn[ix],y1=mCn[ix],
col='#BBBBBB',
lwd=5,) #Om fel, prova ta bort detta komma
par(new=F)
mix <- as.character(mchr)==this$chr
plot(mpos[mix],mval[mix],
pch=16,
cex=2,
cex.lab=3,
#mar=c(0.1,0.1,0.1,0.1),
main = "",
xlab = "",
ylab = "",
col = '#00000010',
xlim = c(0,this$length),
ylim = xlim,
yaxt="n",
xaxt="n")
axis(1,cex.axis=2)
axis(2,cex.axis=2)
mtext(text=paste("Coverage,",this$chr),side=1,line=4,cex=2,las=1)
segments(x0=start[ix],x1=end[ix],
y0=int[ix],y1=int[ix],
col=col,
lwd=4,)
par(new=F)
six <- as.character(schr)==this$chr
plot(spos[six],sval[six],
pch=16,
cex=2,
cex.lab=3,
#mar=c(0.1,0.1,0.1,0.1),
main = "",
xlab = "",
ylab = "",
col = '#00000010',
xlim = c(0,this$length),
ylim = c(0,1),
yaxt="n",
xaxt="n")
axis(1,cex.axis=2)
axis(2,cex.axis=2)
mtext(text=paste("Allelic imbalance,",this$chr),side=1,line=3.5,cex=2,las=1)
segments(x0=start[ix],x1=end[ix],
y0=ai[ix],y1=ai[ix],
col=col,
lwd=4,)
dev.off()
}
}
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