scverse
After removing rows with only NaN interactions, none remain.
Description
...
Minimal reproducible example
import numpy as np
import os
import scanpy as sc
import squidpy as sq
sc.logging.print_header()
print(f"squidpy=={sq.__version__}")
adata = sc.read_h5ad('seqfish.h5ad')
sq.pl.spatial_scatter(
adata, color="celltype_mapped_refined", shape=None, figsize=(10, 10)
)
sq.gr.spatial_neighbors(adata, coord_type="generic")
sq.gr.nhood_enrichment(adata, cluster_key="celltype_mapped_refined")
sq.pl.nhood_enrichment(adata, cluster_key="celltype_mapped_refined", method="ward")
sq.gr.co_occurrence(adata, cluster_key="celltype_mapped_refined")
sq.pl.co_occurrence(
adata,
cluster_key="celltype_mapped_refined",
clusters="Lateral plate mesoderm",
figsize=(10, 5),
)
sq.gr.ligrec(
adata,
n_perms=100,
cluster_key="celltype_mapped_refined",
)
sq.pl.ligrec(
adata,
cluster_key="celltype_mapped_refined",
source_groups="Lateral plate mesoderm",
target_groups=["Intermediate mesoderm", "Allantois"],
means_range=(0.3, np.inf),
alpha=1e-4,
swap_axes=True,
)
Traceback
...
Version
scanpy==1.9.5 anndata==0.9.2 umap==0.5.6 numpy==1.24.3 scipy==1.11.3 pandas==2.2.2 scikit-learn==1.3.0 statsmodels==0.14.1 igraph==0.11.5 pynndescent==0.5.12 squidpy==1.5.0 ...
it seems change the code as following sq.gr.ligrec( adata, n_perms=100, cluster_key="celltype_mapped_refined", use_raw=False, threshold=0 ) sq.pl.ligrec( adata, cluster_key="celltype_mapped_refined", source_groups="Lateral plate mesoderm", target_groups=["Intermediate mesoderm", "Allantois"], means_range=(0.3, np.inf), alpha=1e-4, swap_axes=True, ) but I do not know wthether it is right to set like this, because the tutorial does not do like this
thanks a lot. @LLehner
when I run this code sq.gr.ligrec( adata, n_perms=100, cluster_key="celltype_mapped_refined",
)
Dear @asmlgkj Thank you for providing edited parameters of sq.gr.ligrec function. I had same problem in both seqFISH and Slide-seq tutorials but when I applied use_raw=False and threshold=0 the problem is solved.
https://github.com/scverse/squidpy/issues/871#issuecomment-2326748408 same here
