Question: How to adjust/add cytoband information in specific regions of karyoplot?
1
gravatar for lakhujanivijay
10 months ago by
lakhujanivijay5.3k
India/Ahmedabad
lakhujanivijay5.3k wrote:

Hi

I am trying to plot copy number information using karyoploteR over the karyotype plot; a snapshot of which looks something like this

k

I just want to have the cytoband in the regions where there is either a pink or a green bar. For example, you can notice that there is no cytoband information at the regions where there is a pink rectangle at chr15 in the image. I know we can forcefully add all cytobands but this is not what I want as it become clumsy.

This is how I am plotting.

Plotting the ideogram

kp <- plotKaryotype(genome = "hg19", main="Copy Number data",plot.type=2, plot.params = pp)

Adding the cytoband information

kpAddCytobandLabels(kp)

Could you please help? Tagging bernatgel

karyoploter cnv bioconductor R • 218 views
ADD COMMENTlink modified 10 months ago by zx87549.7k • written 10 months ago by lakhujanivijay5.3k
0
gravatar for zx8754
10 months ago by
zx87549.7k
London
zx87549.7k wrote:

Not tested (will check later when have more time).

kp$cytobands has cytoband ranges, we need to subset by overlap with our pink regions and update, something like:

kp$cytobands <- myRangeMergeByOverlapFun(kp$cytobands, myPinkRanges)

then call:

kpAddCytobandLabels(kp, force.all = TRUE)
ADD COMMENTlink modified 10 months ago • written 10 months ago by zx87549.7k
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