Description Usage Arguments Details Value
This function plots pileups of each selected chromosome
1 2 3 4 5 6 7 8 9 | ave.mean.median(
aveType,
aveLArg,
rc,
pT,
arrowsYes = 0,
offsetf = 1,
noReflect = 1
)
|
aveType |
Average type mean or median |
aveLArg |
A list of chromosomes |
pT |
A list of plot titles |
arrowsYes |
Boolean. 1 = arrows at CHiP sights, 2 = no arrows |
offsetf |
The plot offset. Default = 1 Path to the input file |
noReflect |
Boolean.1 No x axis reflection. 0 means x axis reflection |
save.mean.median <- function(aveType,aveLArg,rc,pT,arrowsYes=0,offsetf=1, noReflect=1){
if (noReflect != 1){
aveLArg[[1]] = ave.filter(list(aveLArg[[1]],inverse.matrix(aveLArg[[1]])),aveType)
aveLArg[[2]] = ave.filter(list(aveLArg[[2]],inverse.matrix(aveLArg[[2]])),aveType)
}
HiC.Plot(matrix.sparse(aveLArg[[1]]),pT[1],arrowsYes,offsetf)
HiC.Plot(matrix.sparse(aveLArg[[2]]),pT[2],arrowsYes,offsetf)
color.bar(maxC,sz)
HiCRatio.Plot(ratioF(aveLArg[[1]],aveLArg[[2]],rc),pT[3],arrowsYes,offsetf)
ratio.color.bar(colorRampPalette(c("red","white","blue"))(shades*2), ratioSBR,round(ratioSBR+1,0))
}
Plots pileups of selected chromosomes.
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