Skip to content

Issue with tl.annotate_cells_cluster function #344

Description

@prasadm1k

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

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions