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jinworks / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
GNU General Public License v3.0
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how to obtain the visium_mouse_cortex_annotated_full.RData in the Spatial vignette? #238

Open pcantalupo opened 1 month ago

pcantalupo commented 1 month ago

Hello, How can I get a copy of the RData that you use in the Spatial vignette?

https://github.com/jinworks/CellChat/blob/main/tutorial/CellChat_analysis_of_spatial_transcriptomics_data.Rmd#L68

sqjin commented 1 month ago

@pcantalupo Please check https://figshare.com/projects/Example_data_for_cell-cell_communication_analysis_using_CellChat/157272

pcantalupo commented 1 month ago

Thank you

Two more things

  1. The RData on Figshare is called visium_mouse_cortex_annotated.RData not the "full" RData (visium_mouse_cortex_annotated_full.RData) as specified in your code. Is it the same one and will it work in the CellChat_analysis_of_spatial_transcriptomics_data.Rmd R markdown file?
  2. How do I get the JSON file? I could find it on FigShare. Here is your code file.path("/Users/suoqinjin/Library/CloudStorage/OneDrive-Personal/works/CellChat/tutorial/spatial_imaging_data_visium-brain", 'scalefactors_json.json'))

If possible, please provide reproducible links to these datasets in your code.

Thank you