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 The version available on PyPI is relatively outdated, so some updates are only available via GitHub through local installation using git clone.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.

[LILI-0000-0002-8173-7367]

Hello, @YifanLu2000 . Thanks for your reply.

Yes, Spateo was installed via PyPI following the tutorial page. And I also tried git clone https://github.com/aristoteleo/spateo-release.git and pip install git+https://github.com/aristoteleo/spateo-release. The conda version also indicates v1.1.0 but it is v0.0.0 in jupyternotebook.

I would like to know the recommend python version, now I am using py3.10 for Spateo. I received an error for sphinx 8.1.3, it requires version less than ver6.

Thank you very much for your time, please let me know when you have the PyPI version updated.

Best regards,
Li Li

[Yin-XN]

Hi, @LILI-0000-0002-8173-7367 .I encountered the same issue as you: 'The conda version also indicates v1.1.0 but it shows as v0.0.0 in Jupyter Notebook.' I wanted to ask if you have found a solution to this?

[CAUiKUN]

I ran into this problem too: Error is: ‘TypeError: scc() got an unexpected keyword argument 'cluster_method'.I wanted to ask if you have found a solution to this? @LILI-0000-0002-8173-7367

[CAUiKUN]

However, I tried it out and found that this issue, "The conda version also indicates v1.1.0 but it shows as v0.0.0 in Jupyter Notebook," does not affect this error: "Error is : TypeError: scc() got an unexpected keyword argument 'cluster_method".