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Fix layer handling in Mixscape.mixscape to resolve errors with adata.raw #636

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merged 1 commit into from
Aug 3, 2024
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Fix layer handling in Mixscape.mixscape to resolve errors with adata.raw #636

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10 changes: 8 additions & 2 deletions pertpy/tools/_mixscape.py
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Original file line number Diff line number Diff line change
Expand Up @@ -227,7 +227,7 @@ def mixscape(
X = adata_comp.layers["X_pert"]
except KeyError:
raise KeyError(
"No 'X_pert' found in .layers! Please run pert_sign first to calculate perturbation signature!"
"No 'X_pert' found in .layers! Please run perturbation_signature first to calculate perturbation signature!"
) from None
# initialize return variables
adata.obs[f"{new_class_name}_p_{perturbation_type.lower()}"] = 0
Expand Down Expand Up @@ -461,7 +461,13 @@ def _get_perturbation_markers(
adata_split = adata[split_mask].copy()
# find top DE genes between cells with targeting and non-targeting gRNAs
sc.tl.rank_genes_groups(
adata_split, layer=layer, groupby=labels, groups=genes, reference=control, method="t-test"
adata_split,
layer=layer,
groupby=labels,
groups=genes,
reference=control,
method="t-test",
use_raw=False,
)
# get DE genes for each gene
for gene in genes:
Expand Down
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