Chord diagram issue: track index

[jerrbearo]

Hi, I'm getting errors when trying to plot the chord diagram in "Inference and analysis of cell-cell communication": for (i in 1:length(object.list)) { netVisual_aggregate(object.list[[i]], signaling = pathways.show, layout = "chord", signaling.name = paste(pathways.show, names(object.list)[i])) } for (i in 1:length(object.list)) { netVisual_chord_cell(object.list[[i]], signaling = pathways.show, layout = "chord", signaling.name = paste(pathways.show, names(object.list)[i])) }

It gives the error for both: Error: not enough space for cells at track index '1'

I saw previously you mentioned to "reduce the parameter values of small.gap and big.gap", but it still does not work.

Could you elaborate on what you meant by using "netVisual_chord_cell and netVisual_chord_gene to control these parameters"? Or of any other suggestions to fix this?

Thank you

[sqjin]

"netVisual_chord_cell and netVisual_chord_gene are two core functions for generating chord diagram, which has more parameters that users can control to custom your plot. Have you tried these two functions with different setting of small.gap and big.gap?

[jerrbearo]

@sqjin I did, I tried changing the values for small.gap and big.gap, but it still said there's not enough space at track index "1". for (i in 1:length(object.list)) { netVisual_chord_cell(object.list[[i]], signaling = pathways.show, layout = "chord", small.gap = 0.1, big.gap = 0.3, signaling.name = paste(pathways.show, names(object.list)[i])) }

Would you know of any other ways to help out? Thanks!

[sqjin]

@jerrbearo This is interesting. If you can share me your object, I can test it. I did not have such issues before.

[mieko-cc]

@jerrbearo This is interesting. If you can share me your object, I can test it. I did not have such issues before.

thanks for your suggestion, but I still counter the same error, could you show us how to solve?

[Ryeeeeeeeeee]

Hello I faced the same problem, is there anyone who has some solutions for this?

[carbycrab]

Hi, I am also having the same problem. Any solutions yet?

[Lisa-Jammy]

Hi, I am also having the same problem. Any solutions yet?

Chord diagram

pathways.show <- c("CXCL") par(mfrow = c(1,2), xpd=TRUE) for (i in 1:length(cco.list)) {

• netVisual_aggregate(cco.list[[i]], signaling = pathways.show, layout = "chord", signaling.name = paste(pathways.show, names(cco.list)[i]))
• } Error: not enough space for cells at track index '1'.

[SamuelAlvarezArguedas]

I have tried all the previous ways to fix this issue but I was not able to do it. If someone could help me, I would really appreciate it! Thanks!