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schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
MIT License
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Plot feature tracks for the query genomes as well? #42

Closed yjx1217 closed 1 year ago

yjx1217 commented 1 year ago

Dear Developer,

Do all tracks for plotting need to be based on the reference genomic coordinate? Could plotsr plot feature tracks for the query genomes as well? It will be great if this is possible.

Thanks for the consideration.

Best, Jia-Xing

mnshgl0110 commented 1 year ago

Currently, only reference genomic coordinates are supported. The issue is that visualising tracks for multiple genomes simultaneously without making the plot incomprehensible is not trivial. However, you can try hacking plotsr like below:

$tracks.txt
# file  name    tags
reference.snps.sorted.bed     REF_SNPs    bw:10000;nc:black;ns:8;nf:Arial;lc:sienna;lw:1;bc:peachpuff;ba:0.5
query.snps.sorted.bed     QRY_SNPs    bw:10000;nc:black;ns:8;nf:Arial;lc:sienna;lw:1;bc:peachpuff;ba:0.5

As long as the chromosome IDs for query track are same as reference genome and the coordinates in the query track file less than the corresponding reference chromosome length, this should work. I have not tested this though :)

yjx1217 commented 1 year ago

Hi @mnshgl0110 ,

Thanks for the tip!

Best, Jia-Xing