Closed jjia1 closed 3 months ago
Hi,
First, thank you for fixing this issue. I think the fix should work, but noticed that you deleted lines 1115-1130 in gen_cross_boundary_correctness
and 1257-1272 in gen_cross_boundary_correctness_test
. These lines obtain the embedding coordinates and velocity arrays from the AnnData object. My apologies if the input argument with the same name, x_emb
, confuses you. Yeah, that was a bad naming and as an input argument it just specifies the key string to obtain the actual embedding coordinates. Please let me know if this makes sense to you.
Thank you!
Hi,
First, thank you for fixing this issue. I think the fix should work, but noticed that you deleted lines 1115-1130 in
gen_cross_boundary_correctness
and 1257-1272 ingen_cross_boundary_correctness_test
. These lines obtain the embedding coordinates and velocity arrays from the AnnData object. My apologies if the input argument with the same name,x_emb
, confuses you. Yeah, that was a bad naming and as an input argument it just specifies the key string to obtain the actual embedding coordinates. Please let me know if this makes sense to you.Thank you!
Thanks @g-yichen. I'll re-add those lines back into the PR to avoid any issues down the line. Please take a look once I've finished. J
Hi @g-yichen I restored the missing lines of code. You can ignore the readme file I just left that for my personal fork. Please let me know if there's any other changes I should make for the PR.
Best, J
Pull request type
Please check the type of change your PR introduces:
What is the current behavior?
Issue Number: #6 PR Number on Fork: fixed neighbors key bug #1
Current error status
What is the new behavior?
Current version
evaluation_utils.py
calls the neighbor indices asadata.uns['neighbors']['indices']
. This doesn't work with newer versions of anndata and/or Scanpy whereadata.uns['neighbors'].keys()
will print out:where the indices are inside of the
connectivities_key
. I found the offending behavior in the following functions:Other information
Output from
Please let me know if you need anything else.