After removing rows with only NaN interactions, none remain.

[asmlgkj]

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

Details

...

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
...

[asmlgkj]

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

[LLehner]

Hi @asmlgkj At what point does the problem appear?

[asmlgkj]

thanks a lot. @LLehner

when I run this code
sq.gr.ligrec(
adata,
n_perms=100,
cluster_key="celltype_mapped_refined",

)

[giovp]

hi @asmlgkj are you using log normalized data?

[MEFarhadieh]

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.

[TTTPOB]

#871 (comment) same here