Open asmlgkj opened 3 months ago
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
Hi @asmlgkj At what point does the problem appear?
thanks a lot. @LLehner
when I run this code sq.gr.ligrec( adata, n_perms=100, cluster_key="celltype_mapped_refined",
)
hi @asmlgkj are you using log normalized data?
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.
Description
...
Minimal reproducible example
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 ...