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saeyslab / multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
GNU General Public License v3.0
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Fig 2b in preprint #34

Closed liaojinyue closed 10 months ago

liaojinyue commented 10 months ago

Hi, thanks for the nice tool.

I found the layout of Fig 2b to be very clear and readable. In comparison, when using the make_ggraph_ligand_target_links() function to generate the plot, the output doesn't quite match the clarity of the preprint. I noticed that Fig 2b was created using Cytoscape, and I was wondering if you could kindly share the code needed to prepare the files for Cytoscape and any details regarding the layout used in Cytoscape.

Thank you so much for considering this request.

Jason

browaeysrobin commented 10 months ago

Hi Jason @liaojinyue

No additional code is necessary. graph_plot$source_df_lt and graph_plot$nodes_df are the two tables you can import in cytoscape as network and node table respectively. To generate the plot in Fig 2B, I used the hierarchical layout for visualization.