filter the most significant ligand and receptors in netVisual_bubble in cell chat
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4 weeks ago
synat.keam ▴ 100

Dear fellows,

Not sure anyone has experienced using cellchat for cell/cell communication.

I run netVisual_bubble and netVisual_chord_gene functions of cellchat to visualize cell communication, but got too many receptor/ligand interaction. I still would like to cover all signalling pathways, but I wanted to keep only the most maximum communication probability. I tried thresh argument, but did not work. Kindly review the attach. The documentation is found here https://rdrr.io/github/sqjin/CellChat/man/netVisual_bubble.html.

netVisual_bubble(cellchat.first.art, sources.use = 3, targets.use = c(0:21),
                  thresh = 0.05, remove.isolate = FALSE)
netVisual_chord_gene(cellchat.first.art, 
                          sources.use = 3, 
                          targets.use = c(0:21), 
                          lab.cex = 0.7,
                          legend.pos.y = 0,
                     small.gap = 2)

Hope you could help!

Kind Regards,

Synat

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