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SCA-IRCM / SingleCellSignalR

R package for Bioconductor submission
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How to make the diagrams in Figure 3F, 3G, 3H? They're so visually informative! #7

Open levinhein opened 4 years ago

levinhein commented 4 years ago

How to make the diagrams in Figure 3F, 3G, 3H? They're so visually informative!

SCA-IRCM commented 4 years ago

Hi, Figure 3F is generated using the mv_interactions() function (ex: mv <- mv_interactions(data, genes, cluster, n=10) displays the 10 most variable interactions). Figure 3H is generated using the intra_network() function (for an example see the User's Guide (https://raw.githubusercontent.com/SCA-IRCM/SingleCellSignalR_v1/master/UsersGuide.html). Figure 3G is more tricky, it's actually generated with Cytoscape (https://cytoscape.org/) using the .graphml output file of the inter_network() function. I let you take a look at the User's Guide and try to process your data with Cytoscape. Don't hesitate to come back if you have other questions. Thank's for using SingleCellSignalR!

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