Seurat Wrapper + Circos visualization

[chrismahony]

I am trying to plot the Circo plot in this vingette, when I run:

circos.par(gap.degree = gaps)
chordDiagram(links_circle, directional = 1,order=order,link.sort = TRUE, link.decreasing = FALSE, grid.col = grid_col,transparency = 0, diffHeight = 0.005, direction.type = c("diffHeight", "arrows"),link.arr.type = "big.arrow", link.visible = links_circle$weight >= cutoff_include_all_ligands,annotationTrack = "grid",
preAllocateTracks = list(track.height = 0.075))

we go back to the first track and customize sector labels

circos.track(track.index = 1, panel.fun = function(x, y) {
circos.text(CELL_META$xcenter, CELL_META$ylim[1], CELL_META$sector.index,
facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.55), cex = 1)
}, bg.border = NA) #

I get :

Error: order should contain names of all sectors.

If you could help me I would really appreciate it, thanks,
Chris

[browaeysrobin]

Hi @chrismahony

This is an error that sometimes can occur when one of the label names is duplicated (probably there might be other reasons also...). In the context of the NicheNet plots, this means that one of the ligands might be belonging to multiple sender cell types, or might also be a target gene or receptor itself in the receiver. You will need to apply a hack and add some whitespace to the symbol name.

We will be working on this to solve this issue automatically, but not in the immediate short term