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dpeerlab / ENVI

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Handle cases where single cell data lacks genes present in spatial data #61

Closed LinearParadox closed 6 months ago

LinearParadox commented 6 months ago

I ran into a bug where this line in the code fails:

self.sc_data = self.sc_data[:, sc_genes_keep]

I believe it's because my single cell data doesn't have all the genes that my spatial data does, and since sc_genes_keep is a union of this with the spatial genes, it causes an index error.

DoronHav commented 6 months ago

Thanks for pointing this bug out to us, we will fix it in the next patch.

For now, you can just manually remove those genes from the spatial data before initializing ENVI and it should work.

DoronHav commented 6 months ago

This was fixed in a new patch