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!

[YifanLu2000]

Hi @LILI-0000-0002-8173-7367, I’d like to know the version of Spateo you’re using. The version available on PyPI is relatively outdated, so some updates are only available via GitHub through local installation using git clone. We apologize for the inconvenience and will update the PyPI version soon.