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SBRG / pymodulon

Python package for analyzing and visualizing iModulons
MIT License
11 stars 13 forks source link

plot_gene_weights() Not working #29

Closed kevin-rychel closed 4 years ago

kevin-rychel commented 4 years ago

I'm getting some very strange matplotlib errors when I try to plot gene weights...

command: plot_gene_weights(ica_data, 79)

image

data.zip

kevin-rychel commented 4 years ago

Oh, I just realized the reason for this: Precise_2 files (received from Cam) were missing gene_info for all pseudogenes, but I think pymodulon threw an error if there wasn't gene info for all genes. I added rows for all pseudogenes, but I didn't fill in the start/stop sites since I didn't know them. The error is happening because it's trying to plot np.nan start locations.

The following code works:

ica.gene_table = ica.gene_table.fillna(0) plot_gene_weights(ica, 79)

I can close this, but I'm curious if anyone has a gene_info file that's more complete than the one Cam is using?

avsastry commented 4 years ago

@camlam should have the correct file. I'd recommending checking the PRECISE 2.0 repo