netvisual_bubble question

[JKarmanAbbVie]

Hi,

I have a cellchat object generated from public data GSE136831.

I ran

cellchat_gse136831_ipf_trimean <- rankNetPairwise(cellchat_gse136831_ipf_trimean) ipf_sig <- identifyEnrichedInteractions(cellchat_gse136831_ipf_trimean, from = 'Macrophage', to = 'Myofibroblast', bidirection = F, thresh = 1e-300)

str(ipf_sig) 'data.frame': 616 obs. of 2 variables: $ ligand : chr "PSAP" "LGALS1" "CD99" "TIMP1" ... $ receptor: chr "LRP1" "ITGB1" "CD99" "CD63" ...

netVisual_bubble(cellchat_gse136831_ipf_trimean, sources.use = 'Macrophage', targets.use = 'Myofibroblast', thresh = 1e-300)

However, if i try to run any signaling pathway clearly present in the plot above, or even L-R pairs from ipf_sig object above, I constantly get

netVisual_bubble(cellchat_gse136831_ipf_trimean, sources.use = 'Macrophage', targets.use = 'Myofibroblast', thresh = 1e-300, signaling = 'EGF') Comparing communications on a single object

Error in subsetCommunication_internal(net, LR, cells.level, slot.name = slot.name, : No significant signaling interactions are inferred based on the input!

Am I missing something?

Thanks,

JK

[sqjin]

@JKarmanAbbVie Does this result from netVisual_bubble(cellchat_gse136831_ipf_trimean, sources.use = 'Macrophage', targets.use = 'Myofibroblast', thresh = 1e-300) look good? I feel there may be a bug when you specifying a signaling.

[JKarmanAbbVie]

Yes, the output without specifying the signaling looks fine.

---

From: Suoqin Jin @.> Sent: Thursday, June 16, 2022 7:05:38 PM To: sqjin/CellChat @.> Cc: Karman, Jozsef @.>; Mention @.> Subject: [EXTERNAL] Re: [sqjin/CellChat] netvisual_bubble question (Issue #433)

@JKarmanAbbViehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FJKarmanAbbVie&data=05%7C01%7Cjozsef.karman%40abbvie.com%7C4d2dad3ffcbf43ba448508da4fecbb7a%7C6f4d03de95514ba1a25bdce6f5ab7ace%7C0%7C0%7C637910175420273122%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=h9UejfVx2bQBv%2Ba04Wia%2BAJxptuuYfqQ0HK67bn4FsI%3D&reserved=0 Does this result from netVisual_bubble(cellchat_gse136831_ipf_trimean, sources.use = 'Macrophage', targets.use = 'Myofibroblast', thresh = 1e-300) look good? I feel there may be a bug when you specifying a signaling.

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