Issue with tl.annotate_cells_cluster function
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prasadm1k commented
Adding this issue on Petra's request.
My UMAP looks as expected (I had already run this analysis previously on besca24ngs)
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.
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