Bernat Gel

Hi @rthapa1 You can visualize CNV data with karyoploteR using any "bed-like" file as an input file or actually anything you can convert into a GRanges in R. However, @miriammagallon...

Hi @rthapa1 Yes, sure, you can plot on any genome with CopyNumberPlots. To do that you need to build a custom genome (for example, a bed-like file with one line...

Hi @cell-c You should be able to find the code you need at the tutorial page (https://bernatgel.github.io/karyoploter_tutorial/). The idea is that you should combine the code to use a custom...

Hi @Rohit-Satyam and @airichli This is a missing option in karyoploteR, and one that should be included. One way to achieve this should be via clipping, but due to limitations...

Hi Diya, TL;DR: You should add `ymax=50000` to your call to `kpPlotBAMDensity`. Full explanation below. I see what your problem is. You have two problems here, actually, a biology/data problem...

Hi @chaomacau I cannot reproduce the problem with a current version of karyoploteR. We had this issue in the past but was solved a few months ago. Could you please...

Hi Joyce, Now I can reproduce. It seems the problem arises from an interaction between selecting a handful of chromosomes and having some of them empty. I'll take a look...

HI @slowkow When I implemented `kpPlotBamCoverage` I was working mainly with exome and genome data and that was not an issue. I see your problem and I think it's an...

Hi @mea2712 1 - It is not possible right now and it might not be possible in the future, due to the complexity it would add to the internal drawing...

Hi Maria, Could you explain me how is svg not working? I use it frequently with karyoploteR and works for me. Does it give you an error message? does it...