sc.pl.heatmap: KeyError: "Values ['CD79A'], are not valid obs/ var names or indices.

[DUAN-GAO]

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Hello, after clustering I am trying to use heatmap to visualize the marker gene but got below error: could anyone help, many thanks.

ax = sc.pl.heatmap(adata,marker_genes_dict,groupby='louvain_r1',save="0.png")

KeyError: "Values ['CD79A'], from ['CD79A', 'MS4A1', 'CD3D', 'CD8A', 'CD8B', 'GNLY', 'NKG7', 'CST3', 'LYZ', 'FCGR3A', 'FCER1A'], are not valid obs/ var names or indices."

Versions

anndata 0.7.5 scanpy 1.6.1

[hyjforesight]

I guess you use the HVGs, change use_raw=True

[Gloriacyy]

@hyjforesight I met similar problem, you're right!! thanks a lot. I have filterd hvgs before sc.tl.rank_genes_groups, adata= adata.raw.to_adata(), then pl.heatmap, it worked

[flying-sheep]

yup! genes you filtered out are not available unless you use use_raw