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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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Manhattan plot X- and Y-axis customization #79

Open mdozmorov opened 2 years ago

mdozmorov commented 2 years ago

It seems the chromosome-specific Manhattan plots are missing X-axis basepair markers (say, in Mb). And, Y-axis is missing CNV numbers (it is possible to figure out where the 2 is, but the CNVs are not immediately obvious). 

cnvpytor -root ${FILEOUT1} ${FILEOUT2} -view 10000
cnvpytor> set chrom chr4
    * chrom: ['chr4']
cnvpytor> manhattan

image

I may be missing something obvious, but I looked at most help pages in interactive mode and couldn't find the solution. Ended up annotating axes manually, but it'll be good to have this functionality.

suvakov commented 2 years ago

Unfortunately, manhattan style plot is made for genome wide plots ant it annotates only chromosome name on X axis. You can use region type plot. Thanks for suggestion abut Y-axis, we will fix it. Btw, you can increase y-axis scale using "rd_manhattan_range" parameter.