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I get an error with my code like this:

for adata in [adata_fish]:
    sc.pp.neighbors(adata, n_neighbors=10, n_pcs=50)
    sc.tl.leiden(adata)

and because of this code I can't run this code:

# Plot Leiden clusters on tSNE 
for adata in [adata_fish]:
    print(adata.uns["name"], ":")
    sc.pl.tsne(adata, color=["leiden"], cmap="tab20")
    sc.pl.tsne(adata, color=markers, layer="sqrt_norm")

which gives me an error message "KeyError: 'Could not find key leiden in .var_names or .obs.columns.'"

Not sure where it went wrong...

Caroline
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0 Answers0