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saezlab / decoupler-py

Python package to perform enrichment analysis from omics data.
https://decoupler-py.readthedocs.io/
GNU General Public License v3.0
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PLOT issues #114

Closed Sophon-0 closed 6 months ago

Sophon-0 commented 6 months ago

Hello,

1) The ANOVA plot does not provide enough colors to differentiate the cell types. is there an option to add our own colors ? And it's even confusing with the conditions. 2) The dc.plot_network is not giving the same output as the tutorial. The whole plot is either green or dark blue, based on the gene expression log2FC, I assume. Basically, I don't see any label nor edges, I just see an ocean of green and the names of the TF and genes on it.

Thanks

PauBadiaM commented 6 months ago

Hi @AgentScientist,

  1. ANOVA plot: you can change the cmap_cats to use your preferred colormap for categories, you can even pass a custom one.
  2. Network plot: Depending on the igraph and matplotlib version you have the scales change completely, you can play with the node_size parameter to see if your nodes are either too big or too small.

Hope this is helpful!

Sophon-0 commented 6 months ago

Thanks a lot ! The default node size was 100