Hello,

I have a question about R visualization using Circlize package.

I tried to use Circos but it was pretty hard for me so instead I used Circlize package in R.

I made my plot using this script :

library(circlize)
library(extrafont)


#read the csv file
data <- read.csv("/circos/chord2.csv", row.names = 1)

#convert the table to a martix
data <- as.matrix(data)

#assign color to each group of strains
col = c(systemdevelopment = "#488FCD", 
        vasculaturedevelopment = "#FEC111", 
        multicellularorganismdevelopment = "#90419A", 
        tubedevelopment = "#EF3A67",
        musclestructuredevelopment = "#99CC00",
        circulatorysystemdevelopment = "#39C0C4",
        cellpopulationproliferation = "#F16739",
        tissuedevelopment = "#607D8B",
        celldifferentiation = "#FF3300", 
        SERPINE1 = "grey",
        ANXA1 = "grey",
        TAGLN2 = "grey",
        BLOC1S2 = "grey",
        APELA = "grey",
        SRSF1 = "grey",
        NPPB = "grey",  
        SHTN1 = "grey",
        GREM1 = "grey",
        PIK3C2A = "grey",
        HMOX1 = "grey",
        HES3 = "grey",
        HOMER1 = "grey",
        ATF5 = "grey",
        CUZD1 = "grey",
        TJP1 = "grey",
        ACVR1B = "grey",
        PLAU = "grey",
        ARFRP1 = "grey",
        TRIM54 = "grey",
        CASP3 = "grey", 
        CD164 = "grey",
        DDIT4 = "grey",
        VIM = "grey",
        SCN8A = "grey",
        MMP24 = "grey",
        CAV1 = "grey",
        SLC7A11 = "grey",
        SKIL = "grey",
        SP3 = "grey",
        TWIST1 = "grey"
        )

#create a chord diagram but without labeling 
cir <- chordDiagram(data, grid.col = col, 
             annotationTrack = c("grid"), 
             preAllocateTracks = 1,
             transparency = 0.2,
             h.ratio = 0.4,
             big.gap = 1,
             small.gap = 1
             )


#add the labels and axis
cir <- circos.trackPlotRegion(track.index = 2, panel.fun = function(x, y) {
  xlim = get.cell.meta.data("xlim")
  ylim = get.cell.meta.data("ylim")
  sector.name = get.cell.meta.data("sector.index")

  #print labels 
  circos.text(mean(xlim), ylim[1] + 2.5, sector.name, 
              facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5), cex=0.6)
  })
  #print axis
#  circos.axis(h = "top", labels.cex = 0.5, major.tick.percentage = 0.2, 
#              sector.index = sector.name, track.index = 2)
#}, bg.border = NA)

And this is the result of this script :

The question that I want to ask is...

Is there any way for making a heat map color of each gene's expression instead of the grey in each bar at the rim of the circle indicating each gene?

I saw that in other plots using Circos. But I want to know I can make it with this package.

Thank you!