Bernat Gel

Glad it worked :) On Thu, Sep 5, 2019 at 7:07 PM Richard James Acton wrote: > Hi @bernatgel Thanks a lot for the help. I > think I was...

Hi @repeatpipettor I cannot reproduce the error. Mixing the example above with the example code in kpPlotGenes it just works. ``` library(karyoploteR) library(ggplotify) pp

Hi @mvapontes I think your problem here is a typo. Have you tried to run the karyoploteR code by itself out of the `expression` and `as.ggplot`? I've copied the code...

Ok, I've downloaded the data and can reproduce the problem. With a human genome and my BAMs it works ok, but not with your genome and BAMs... I'll investigate to...

Hi @etnite One option would be to add some enlarge the margin between chromosomes to add some space for the base numbers using [setting the plotting parameters](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotParams/PlotParams.html). ``` pp

Hi Johannes, Actually, the transcripts do not overlap other transcripts (or at least should not) but the transcript positioning algorithm does not take into account the labels. This is something...

Yes, thisis one of karyoploteR's most pressing issues. Gene/transcript label overlaps and gene/transcript associated issues. I'll try to work it out in the next few months, although if anyone has...

Hi @Maillinia I was checking that and karyoploteR uses Rsamtools to interact with the BAM files, so it could be a problem if Rsamtools does not support CSI indexes. I'll...

This is not possible yet. And it's much more complex than it would seem. If you take a look at the karyoploteR internal code you can see some commented out...

Hi @raunakms It is currently not possible to pass multiple values to it, but it would certainly be a very good additional kpPlotLinks indeed. I'll add it to the TODO...