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Fix pandas Series used as numpy array index #435

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Merged
vitkl merged 1 commit into from
Feb 22, 2026
Merged

Fix pandas Series used as numpy array index #435

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8 changes: 6 additions & 2 deletions cell2location/plt/plot_expected_vs_obs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,12 @@ def plot_expected_vs_obs(
# extract from anndata and convert to numpy if needed
x = data[:, gene1].X
y = data[:, gene2].X
x_mu = mu[:, np.where(data.var_names == gene1)][mu[:, np.where(data.var_names == gene1)] > 0].flatten()
y_mu = mu[:, np.where(data.var_names == gene2)][mu[:, np.where(data.var_names == gene2)] > 0].flatten()
x_mu = mu[:, np.where(np.array(data.var_names == gene1))][
mu[:, np.where(np.array(data.var_names == gene1))] > 0
].flatten()
y_mu = mu[:, np.where(np.array(data.var_names == gene2))][
mu[:, np.where(np.array(data.var_names == gene2))] > 0
].flatten()

from anndata._core.views import SparseCSRView
from scipy.sparse.csr import csr_matrix
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2 changes: 1 addition & 1 deletion cell2location/run_colocation.py
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Expand Up @@ -376,7 +376,7 @@ def run_colocation(
if sc_spatial_present:
sc.settings.figdir = fig_path

s_ind = sp_data.obs[train_args["sample_name_col"]] == s
s_ind = (sp_data.obs[train_args["sample_name_col"]] == s).values
s_keys = list(sp_data.uns["spatial"].keys())
s_spatial = np.array(s_keys)[[s in i for i in s_keys]][0]

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2 changes: 1 addition & 1 deletion docs/notebooks/tutorial_utils.py
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Expand Up @@ -16,7 +16,7 @@ def plot_genes_per_cell_type(slide, genes, ctypes):
# limit color scale at 99.2% quantile of gene expression (computed across cell types)
quantile_across_ct = np.array(
[
np.quantile(slide.layers[n][:, slide.var["SYMBOL"] == genes[j]].toarray(), 0.992)
np.quantile(slide.layers[n][:, (slide.var["SYMBOL"] == genes[j]).values].toarray(), 0.992)
for n in slide.uns["mod"]["factor_names"]
]
)
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