scverse / scverse/squidpy

pl.ligrec does not match pvaule table output

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Description

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Hi all,

I'm still new to bioinformatics and coding, having the following problem:
First of all I was wondering how it is possible that pvalues can be exactly 0.
Based on this observation, the plot of the interactions seems to be off. I noticed for one interaction pair that the values in the pvalues table are either 0 or NaN. In the plot however the dots for the 0 values are marked as not significant. Thanks for your help in advance :)

I used the following code:

res = sq.gr.ligrec( adata, cluster_key="celltype", n_perms=500, threshold=0.05, copy=True, use_raw=True )

sq.pl.ligrec( res, alpha=0.05, swap_axes=False, means_range=(1, np.inf), target_groups="C LAM" )

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Research direction

Reproduce the reported sq.gr.ligrec and sq.pl.ligrec calls using the supplied parameters, then compare the pvalues table with the plotted significance markers for zero and NaN values. Done means determining why the table and plot disagree and adding or updating coverage so their handling is consistent.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, data-visualization
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
35/100

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