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Allow different criteria to select genes #126

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Allow different criteria to select genes #126

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6257462
Update utils.py
HelloWorldLTY Dec 14, 2024
a59f125
Update mapping_utils.py
HelloWorldLTY Dec 14, 2024
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6 changes: 3 additions & 3 deletions tangram/mapping_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
logging.getLogger().setLevel(logging.INFO)


def pp_adatas(adata_sc, adata_sp, genes=None, gene_to_lowercase = True):
def pp_adatas(adata_sc, adata_sp, genes=None, gene_to_lowercase = True, min_cells=1):
"""
Pre-process AnnDatas so that they can be mapped. Specifically:
- Remove genes that all entries are zero
Expand All @@ -37,8 +37,8 @@ def pp_adatas(adata_sc, adata_sp, genes=None, gene_to_lowercase = True):
"""

# remove all-zero-valued genes
sc.pp.filter_genes(adata_sc, min_cells=1)
sc.pp.filter_genes(adata_sp, min_cells=1)
sc.pp.filter_genes(adata_sc, min_cells=min_cells)
sc.pp.filter_genes(adata_sp, min_cells=min_cells)

if genes is None:
# Use all genes
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4 changes: 2 additions & 2 deletions tangram/utils.py
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Expand Up @@ -338,7 +338,7 @@ def deconvolve_cell_annotations(adata_sp, filter_cell_annotation=None):
return adata_segment


def project_genes(adata_map, adata_sc, cluster_label=None, scale=True):
def project_genes(adata_map, adata_sc, cluster_label=None, scale=True, min_cells=1):
"""
Transfer gene expression from the single cell onto space.

Expand All @@ -359,7 +359,7 @@ def project_genes(adata_map, adata_sc, cluster_label=None, scale=True):
adata_sc.var_names_make_unique()

# remove all-zero-valued genes
sc.pp.filter_genes(adata_sc, min_cells=1)
sc.pp.filter_genes(adata_sc, min_cells=min_cells)

if cluster_label:
adata_sc = mu.adata_to_cluster_expression(adata_sc, cluster_label, scale=scale)
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