spateo.tl.scc

[LILI-0000-0002-8173-7367]

Hello, Spateo team.

Thank you very much for developing this wonderful tool.

I noticed that the tl.scc function does not work in my end. Would you please let me know how to correct it? Thank you.

import spateo as sp
......
sp.tl.scc(
    ms_data,
    s_neigh=8,
    e_neigh=30,
    resolution=2,
    cluster_method="leiden",
    key_added="scc",
    pca_key="pca",
)

Error is : TypeError: scc() got an unexpected keyword argument 'cluster_method'

[LILI-0000-0002-8173-7367]

If I omit cluster_method="louvain", the program stops at spatial_neighbors.params and keep running overnight.

[LILI-0000-0002-8173-7367]

Hello, Spateo team.

I also noticed two more issues.

1. Spateo version
   I installed spateo v1.1.0, but it indicated 0.0.0 in jupyternotebook.
   

2. STAGATE Clustering function
   I tried to switch to STAGATE Clustering function.

sp.pp.select_hvf_seurat(adata,n_top= 2000,)

gave me an error.

AttributeError: module 'spateo.pp' has no attribute 'select_hvf_seurat'

Thanks for your time and help!

Cheers,
Li Li

[Xiaojieqiu]

thanks LiLi, @YifanLu2000 Yifan will work on this!