Question: KaryoplotR, display 2 different chromosome scales on the same plotKaryotype
0
gravatar for Bastien Hervé
2.6 years ago by
Bastien Hervé4.8k
Karolinska Institutet, Sweden
Bastien Hervé4.8k wrote:

First of all, I post my question here following KaryoplotR tutorial instructions ( https://bernatgel.github.io/karyoploter_tutorial/ )

More information at the karyoploteR Bioconductor page and at the karyoploteR github repo or asking a question at biostars.

I want to create a custom.genome with this GRanges :

GRanges object with 2 ranges and 0 metadata columns:
   seqnames            ranges            strand
      <Rle>           <IRanges>           <Rle>
    chr12_IgH   [113200000, 113550000]      *
    chr6_IgH    [70720000, 71150000]        *

When I display my custom.genome I got something like this :

kp <- plotKaryotype(genome = custom.genome)

star multiqc

If I display solo either chr12_IgH or chr6_IgH I got a correct rectangle bar like this :

GRanges object with 1 range and 0 metadata columns:
   seqnames            ranges            strand
      <Rle>           <IRanges>           <Rle>
    chr6_IgH    [70720000, 71150000]        *

Command line to display :

kp <- plotKaryotype(genome = custom.genome)

star multiqc

And, if I change my chr6_IgH IRanges to get closer to chr12_IgH :

GRanges object with 2 ranges and 0 metadata columns:
   seqnames            ranges            strand
      <Rle>           <IRanges>           <Rle>
    chr12_IgH   [113200000, 113550000]      *
    chr6_IgH    [113000000, 113200000]      *

Command line to display :

kp <- plotKaryotype(genome = custom.genome)

star multiqc

The visualization is good !

I'm looking for a way to apply different scales on my chromosomes to fit my first GRanges, is there a way to do it ?

(Feel free to move this thread, if it's not appropriate here)

Thanks !

karyoplotr R • 734 views
ADD COMMENTlink modified 2.5 years ago • written 2.6 years ago by Bastien Hervé4.8k
0
gravatar for Bastien Hervé
2.5 years ago by
Bastien Hervé4.8k
Karolinska Institutet, Sweden
Bastien Hervé4.8k wrote:

Short answer from @bernatgel on github : It's not possible yet

Detailled answer : https://github.com/bernatgel/karyoploteR/issues/9

ADD COMMENTlink written 2.5 years ago by Bastien Hervé4.8k
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