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Issue with tl.annotate_cells_cluster function #344

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prasadm1k opened this issue May 30, 2024 · 0 comments
Open

Issue with tl.annotate_cells_cluster function #344

prasadm1k opened this issue May 30, 2024 · 0 comments

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@prasadm1k
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Adding this issue on Petra's request.

My UMAP looks as expected (I had already run this analysis previously on besca24ngs)

image

The issue occurs when I label my celltypes and then re-plot the UMAP with the labels. I get the following gibberish. I know that the labelings are good.

image (1)

The problem was sorted by using a different labelling function as described by Petra.

Dictionary for renaming values

correspondence = {
'0': 'Tumor_Necro',
'1': 'Tumor',
'2': 'Tumor_Necro',
'3': 'Tumor_Fibro',
...
}

adata.obs['annov2'] = adata.obs['leiden'].copy()
adata.obs['annov2'] = adata.obs['annov2'].replace(correspondence)

So seems like an issue with the tl.annotate_cells_cluster function

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