Color coding Sectors

[Veracity2693]

Hi,

Thank you for a wonderful package for visualization and making it public for everyone's use.

I have come across an error that I am looking for some help on.

I tried using ColorRamp2 to give a range of colors to sectors but it gives the following error:
Error in rep(grid.col, n) :
attempt to replicate an object of type 'closure'

Pardon me for my beginner-level knowledge in R.

[jokergoo]

Can you tell me how you use the function? Maybe you can paste your full set of code here.

[Veracity2693]

id	size
Reg. of cell populationproliferation	23.75742587
Pos. reg. of gene expression	21.46836412
Pos. reg. of developmentalproc.	21.46836412
Pos. reg. of RNA metabolicproc.	22.66607561
Epithelium development	21.46836412
Reg. of multicellularorganismal development	21.46836412
Pos. reg. of cell populationproliferation	20.13798421
Tissue morphogenesis	18.63679501
Animal organ morphogenesis	20.13798421
Reg. of protein modificationproc.	21.46836412
Pos. reg. of transcription,DNA-templated	21.46836412
Pos. reg. of nucleicacid-templated transcription	21.46836412
Pos. reg. of RNA biosyntheticproc.	21.46836412
Reg. of transferase activity	19.15922786
Reg. of kinase activity	18.63679501
Cytokine-mediated signalingpathway	19.15922786
Reg. of protein kinaseactivity	18.0891648
Pos. reg. of molecularfunction	21.46836412
Epithelial celldifferentiation	18.63679501

This is the df2 data frame and the corresponding values which I tried making a color ramp with and used the code as following

library(circlize)

Or use a data frame

df = read.table("Chord_GO_KEGG.txt",sep='\t', header = TRUE)
df2 = read.table("SectorValues.txt",sep='\t', header = TRUE)

grid.col = colorRamp2(range(df2["size"]), c("#004bff", "#bfd2ff"), transparency = 0.1)

col_fun = colorRamp2(range(df["value"]), c("#FFEEEE", "#FF0000"), transparency = 0.1)

#chordDiagram(df, grid.col = grid.col, col = col_fun)

png("Chord_Diagram_GO_KEGG.png", units = "in", width = 15.5, height = 16.5, res=1200)

chordDiagram(df, grid.col = grid.col, col = col_fun, annotationTrack = c("grid"), annotationTrackHeight = mm_h(10), link.border="white", link.zindex = rank(df["value"]), link.sort = TRUE, link.decreasing = TRUE)

dev.off()
circos.track(track.index = 1, panel.fun = function(x, y) {
circos.text(CELL_META$xcenter, CELL_META$ylim[1], CELL_META$sector.index,
facing = "reverse.clockwise", niceFacing = TRUE, adj = c(0, 0.5))}, bg.border = NA)

circos.clear()

If I need to post other files, please let me know. And thank you again for trying to help me

[jokergoo]

chordDiagram(df, grid.col = grid.col, ...

Argument grid.col can only be set to a vector of colors. The object grid.col you generated with colorRamp2() is a color mapping function. Maybe you can do:

grid.col = colorRamp2(range(df2["size"]), c("#004bff", "#bfd2ff"), transparency = 0.1)(df2["size"])
names(grid.col) = df2[, 1]. ## now grid.col is a named vector
chordDiagram(df, grid.col = grid.col, ...