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.
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