Without X_umap in obsm of output adata

[houruiyan]

Hello, I am sorry to bother you again.
When I finish running SCALEX, I found that adata did not include X_umap in obsm. Is this right? I remember l can directly get X_umap in obsm layer. This is my output adata structure.

Something changed? or I remember wrong?

Thank you in advance.
Ruiyan

[jsxlei]

Hi Ruiyan, did you have umap.png in your outdir where adata is located? The reason may be because sc.pl.umap was not activated in SCALEX in your case. Here what I am testing is right. The adata should have

It would be helpful if you could your command or the way how you run SCALEX.

[houruiyan]

Thank you for your reply!

Yes, I have the umap.png in my outdir. Here is my command.
nohup SCALEX.py --data_list final_cave.h5ad final_surface.h5ad final_zebrafish.h5ad --batch_categories cave surface zebrafish --outdir ./SCALEX_out/ &

This is my output file.

Thank you!
Ruiyan

[jsxlei]

Could you also provide the SCALEX version? It is really wierd that there is no X_umap in adata after plotting the umap.png since it will not be deleted.

[houruiyan]

I am sorry for late reply. Now, I think it is ok when I update the SCALEX version by using
pip install git+https://github.com/jsxlei/scalex.git .

I think the v1.0.0 may produce the problem that I report.
Thank you very much for your warm help.