Bernat Gel

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icon company Germans Trias Research Institute (IGTP) icon location Barcelona, Spain icon location Bioinformatician at IGTP. Interested in cancer genomics, data analysis and visualization. Working on NF1, Hereditary Cancer and genetic diagnostics.

Results 46 comments of Bernat Gel

kpPlotDensity log scaling?

Hi @aboyd003 It is indeed not possible to set up a log scale for kpPlotDensity. To do it right, we should probably use the log capabilities of base R and...

kpPlotDensity log scaling?

Great! glad that helped! I've added the log scale to the list of future enhancements, but much better if you do not need to wait for me! Bernat El jue,...

Align ideograms to the right side

Hi @abs-yy No, right now it's not possible. It could be implemented, but it means adding a new coordinate transformation function on the guts of karyoploteR. What's the use case?...

Question on Removing Cytoband Borders in karyoploteR

Hi @hj-99 Sure, you can do that. The trick is using the function to plot the cytobands independently. kpPlotKaryotype can plot the cytobands and can accept a bit of customization....

makeGenesDataFromTxDb did not pick up gene in some region

Hi @h20gg702 and Guillermo @GRealesM Thanks for pointing this out and for the additional information provided by Guillermo. It seems like a bug in karyoploteR, so I'll have to take...

Cytoband Borders

Yes, there are different ways to do that. The easiest one should be to pass a "border=NA" to plotKaryoptype. That should do the trick. If this does not work (I...