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jsxlei / SCALEX

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
BSD 3-Clause "New" or "Revised" License
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Without X_umap in obsm of output adata #12

Closed houruiyan closed 1 year ago

houruiyan commented 1 year ago

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. image Something changed? or I remember wrong?

Thank you in advance. Ruiyan

jsxlei commented 1 year ago

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

Screen Shot 2022-10-27 at 05 24 50

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

houruiyan commented 1 year ago

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/ &

image This is my output file.

Thank you! Ruiyan

jsxlei commented 1 year ago

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 commented 1 year ago

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.