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Merge pull request #1 from alexanderchang1/alexanderchang1-visum-gexFix
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Update readwrite.py
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alexanderchang1 authored Oct 11, 2024
2 parents be99b23 + 0b89362 commit 33d2591
Showing 1 changed file with 6 additions and 1 deletion.
7 changes: 6 additions & 1 deletion src/scanpy/readwrite.py
Original file line number Diff line number Diff line change
Expand Up @@ -360,6 +360,7 @@ def read_visium(
count_file: str = "filtered_feature_bc_matrix.h5",
library_id: str | None = None,
load_images: bool | None = True,
gex_only: bool = True,
source_image_path: Path | str | None = None,
) -> AnnData:
"""\
Expand All @@ -385,9 +386,13 @@ def read_visium(
'filtered_feature_bc_matrix.h5' or 'raw_feature_bc_matrix.h5'.
library_id
Identifier for the visium library. Can be modified when concatenating multiple adata objects.
gex_only
Only keep 'Gene Expression' data and ignore other feature types,
e.g. 'Antibody Capture', 'CRISPR Guide Capture', or 'Custom'
source_image_path
Path to the high-resolution tissue image. Path will be included in
`.uns["spatial"][library_id]["metadata"]["source_image_path"]`.
Returns
-------
Expand Down Expand Up @@ -420,7 +425,7 @@ def read_visium(
Spatial spot coordinates, usable as `basis` by :func:`~scanpy.pl.embedding`.
"""
path = Path(path)
adata = read_10x_h5(path / count_file, genome=genome)
adata = read_10x_h5(path / count_file, genome=genome, gex_only=gex_only)

adata.uns["spatial"] = dict()

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