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arzwa / wgd

Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd.
http://wgd.readthedocs.io/en/latest/
GNU General Public License v3.0
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Alternative Ks distribution display #86

Open romseg opened 1 year ago

romseg commented 1 year ago

Dear author,

Thanks for creating such a useful program. I was wondering if there is a way to display the Ks distribution as a scatter with continues line figure instead of a histogram with bars without bokeh and just with "wgd viz"? And also density instead of duplicates on the Y axis without bokeh? I know histograms with duplicates in the Y axis can be created without bokeh and it would wonderful to have the above alternatives as well since that is more standard for publication. I really can't install bokeh but I wouldn't really needed if I could produce the alternative with "wgd viz" only. Thanks again.

Rom

heche-psb commented 1 year ago

Hi, it's not a common practice to draw Ks distribution in scatter plot. But I guess it could help if there is a density option as you mentioned.

romseg commented 1 year ago

Dear author,

Please, would it be possible for you to add these options to wgd without bokeh? or at least density option? Thank you for creating such a useful program.

plot1 plot2
heche-psb commented 1 year ago

In fact, I have implemented more sophisticated plot function in v2. You can decide the plot by adding options spair, plotkde, etc. Maybe you can give it a try.

romseg commented 1 year ago

I was not aware of the v2 version. I will give it a try. Thanks.

Rom