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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Heatmap borders per sample #610

Closed Aikaterini-Chatzipli closed 3 years ago

Aikaterini-Chatzipli commented 3 years ago

Hello,

I run CNVkit on targeted sequencing data and generated a CN heatmap. I plotted approximately 90 samples in the heatmap which would be very useful to visualize having lines as borders separating the data per sample across all chromosomes. It's not easy to see where the borders of each sample are when plotting many samples on the same heatmap. Is there currently an option not obvious to me doing what I am describing? Please advise.

Many thanks,

Katerina

tskir commented 3 years ago

Hi @Aikaterini-Chatzipli! Your suggestion makes sense, but I'm afraid there isn't an option available to do this right now. I also only have a very limited time per week to dedicate to CNVkit, so it's unlikely that this is going to be implemented in the foreseeable future.

I'm going to leave this issue up as an enhancement with a help-wanted flag. In case we have any volunteers in the audience to dig into the CNVkit plotting system and add this feature, it would be very much appreciated!

tetedange13 commented 3 years ago

Hi @tskir (and @Aikaterini-Chatzipli ),

A possible easy way to do it, is to add : axis.axhline(i, color='k'), right after L92 of heatmap.py => Do you want me to do a PR for with just this line ? (I can try to create one if you tell me so) => I can also add a dedicated flag parameter to the heatmap subcommand, like --delimit_samples or so

Have a nice day. Kind regards. Felix

Aikaterini-Chatzipli commented 3 years ago

Many thanks to both for your responses!

Dear Felix,

Yes, it would be great if you could please modify the code by adding an extra parameter to it.

Thanks and best wishes,

Katerina