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StatBiomed / SpatialDM

Spatial direct messaging detected by bivariate Moran
https://spatialdm.readthedocs.io
Apache License 2.0
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spatialdm_global does not work with a list of specified index, pair_selection_matrix would change adata #6

Open wyq977 opened 1 year ago

wyq977 commented 1 year ago

Hi I found out there's a bug in spatialdm_global https://github.com/StatBiomed/SpatialDM/blob/aa1762496437a45787314a27e88313bdec6287c0/spatialdm/main.py#L155

For example, if there are 400 lr pairs after extract_lr, one select 10 pairs for computation.

User cannot specify specified_ind as in globle_st_compute(adata) would also be still 400 (or 400x400)

That would throw a error in calculation due to 

adata.uns['global_stat']['z']['st'].shape != np.zeros(total_len).shape

Also in this function, it would change/remove the ligand, receptor and geneInter in adata. Namely, the changes to adata would NOT be local.

For example, if one only specify 2 pairs, after calculation, ligand, receptor and geneInter would be reduced to 2.

You have to re-run extract_lr to get the full list. https://github.com/StatBiomed/SpatialDM/blob/aa1762496437a45787314a27e88313bdec6287c0/spatialdm/utils.py#L92

wyq977 commented 1 year ago

I tried to fix the first problem in this commit https://github.com/StatBiomed/SpatialDM/commit/7bdcaa1e928400cffdc28a111f17822d07638210