Receptor-ligand analysis cannot be reproduced

[Amberzhang66]

Dear authors,

Description

I'm following your tutorial:
https://squidpy.readthedocs.io/en/stable/notebooks/examples/graph/compute_ligrec.html

However, I cannot reproduce it.

When running:

sq.pl.ligrec(res, source_groups="Erythroid", alpha=0.005)

I encountered errors below:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[7], line 1
----> 1 sq.pl.ligrec(res, source_groups="Erythroid", alpha=0.005)

File [~/.conda/envs/py39_2/lib/python3.9/site-packages/squidpy/pl/_ligrec.py:296](https://ondemand.carc.usc.edu/node/a03-10.hpc.usc.edu/49178/lab/tree/~/.conda/envs/py39_2/lib/python3.9/site-packages/squidpy/pl/_ligrec.py#line=295), in ligrec(adata, cluster_key, source_groups, target_groups, means_range, pvalue_threshold, remove_empty_interactions, remove_nonsig_interactions, dendrogram, alpha, swap_axes, title, figsize, dpi, save, **kwargs)
    293 pvals = pvals[pvals <= pvalue_threshold]
    295 if remove_empty_interactions:
--> 296     pvals, means = filter_values(pvals, means, mask=~(pd.isnull(means) | pd.isnull(pvals)), kind="NaN")
    297 if remove_nonsig_interactions and alpha is not None:
    298     pvals, means = filter_values(pvals, means, mask=pvals <= alpha, kind="non-significant")

File [~/.conda/envs/py39_2/lib/python3.9/site-packages/squidpy/pl/_ligrec.py:206](https://ondemand.carc.usc.edu/node/a03-10.hpc.usc.edu/49178/lab/tree/~/.conda/envs/py39_2/lib/python3.9/site-packages/squidpy/pl/_ligrec.py#line=205), in ligrec.<locals>.filter_values(pvals, means, mask, kind)
    203 means = means.loc[mask_rows]
    205 if pvals.empty:
--> 206     raise ValueError(f"After removing rows with only {kind} interactions, none remain.")
    208 mask_cols = mask.any(axis=0)
    209 pvals = pvals.loc[:, mask_cols]

ValueError: After removing rows with only NaN interactions, none remain.

Could you please help with the problem here? Thank you so much!

[selmanozleyen]

this should be solved with #991