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matsengrp / gctree

GCtree: phylogenetic inference of genotype-collapsed trees
https://matsengrp.github.io/gctree
GNU General Public License v3.0
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Tree visualization without the number text #119

Closed markutz556 closed 8 months ago

markutz556 commented 1 year ago

Hi,

Thanks for the tools and it's a great tools for BCR phylogeny analysis.

I generated a BCR tree image with pie chart and the image would become very wide if there are lots of groups (because there is a long list of group number to show on image and it has to be wide to avoid overlap). I think right now the image shows the texts of different groups by default. I wonder if you can make it as an option so that I can choose not to show the number text. Thanks.

Also I got errors when the node name is integer and no errors when the node name is string (same data).

Best, Mike

wsdewitt commented 1 year ago

Hi Mike,

I believe this is the section of code related to the pie chart and its labeling: https://github.com/matsengrp/gctree/blob/23a71520af416e5022981d9bf80f9a8511273859/gctree/branching_processes.py#L501-L518

You could try removing the lines about the text face T in a local clone of gctree, as a workaround.

We could eventually add a new option abundance_labels in the render() command (True by default), such that abundance labels are only produced if abundance_labels=True. We'd also apply this to the non-piechart labels on this line: https://github.com/matsengrp/gctree/blob/23a71520af416e5022981d9bf80f9a8511273859/gctree/branching_processes.py#L493

markutz556 commented 1 year ago

Thanks for the response. I will do that.