A Promlem when read_visium

QIFEIDKN / STAGATE

Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics

MIT License

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A Promlem when read_visium #3

Closed xiao-kong-long closed 2 years ago

xiao-kong-long commented 2 years ago

hello，I meet a problem when run this code: adata = sc.read_visium(path=input_dir, count_file=section_id+'_filtered_feature_bc_matrix.h5') cause this error as follows: OSError: Data\151676\151676_filtered_feature_bc_matrix.h5 does not exist I don't know how can I solve this problem

xiao-kong-long commented 2 years ago

I don't know whether the path Data\151676\151676_filtered_feature_bc_matrix.h5 is wrong?

xiao-kong-long commented 2 years ago

I got the answer, I don't create local directory Data, but another problem occurs, could you provide dataset? I can't find csv and json files in this website, I think it's complex for me, thanks!

QIFEIDKN commented 2 years ago

The spatial information of DLPFC dataset can be found at https://github.com/JinmiaoChenLab/SEDR_analyses/tree/master/data/DLPFC.

xiao-kong-long commented 2 years ago

Thanks for you replay! Thanks!