Chord Diagram: hiding arrows directing to the same sector

Question

Is there a way for hiding those arrows that point to the same chord diagram sector? Meaning that the chord diagram shows only migration to other continents but includes a non-arrowed area which represents intra-continent migration.

These arrows should be deleted or hided

Code

The code is taken from here: https://www.data-to-viz.com/graph/chord.html

    # Libraries
library(tidyverse)
library(viridis)
library(patchwork)
library(hrbrthemes)
library(circlize)
library(chorddiag)  #devtools::install_github("mattflor/chorddiag")

    # Load dataset from github
data <- read.table("https://raw.githubusercontent.com/holtzy/data_to_viz/master/Example_dataset/13_AdjacencyDirectedWeighted.csv", header=TRUE)

# short names
colnames(data) <- c("Africa", "East Asia", "Europe", "Latin Ame.",   "North Ame.",   "Oceania", "South Asia", "South East Asia", "Soviet Union", "West.Asia")
rownames(data) <- colnames(data)

# I need a long format
data_long <- data %>%
  rownames_to_column %>%
  gather(key = 'key', value = 'value', -rowname)

# parameters
circos.clear()
circos.par(start.degree = 90, gap.degree = 4, track.margin = c(-0.1, 0.1), points.overflow.warning = FALSE)
par(mar = rep(0, 4))

# color palette
mycolor <- viridis(10, alpha = 1, begin = 0, end = 1, option = "D")
mycolor <- mycolor[sample(1:10)]

# Base plot
chordDiagram(
  x = data_long, 
  grid.col = mycolor,
  transparency = 0.25,
  directional = 1,
  direction.type = c("arrows", "diffHeight"), 
  diffHeight  = -0.04,
  annotationTrack = "grid", 
  annotationTrackHeight = c(0.05, 0.1),
  link.arr.type = "big.arrow", 
  link.sort = TRUE, 
  link.largest.ontop = TRUE)

# Add text and axis
circos.trackPlotRegion(
  track.index = 1, 
  bg.border = NA, 
  panel.fun = function(x, y) {
    
    xlim = get.cell.meta.data("xlim")
    sector.index = get.cell.meta.data("sector.index")
    
    # Add names to the sector. 
    circos.text(
      x = mean(xlim), 
      y = 3.2, 
      labels = sector.index, 
      facing = "bending", 
      cex = 0.8
      )

    # Add graduation on axis
    circos.axis(
      h = "top", 
      major.at = seq(from = 0, to = xlim[2], by = ifelse(test = xlim[2]>10, yes = 2, no = 1)), 
      minor.ticks = 1, 
      major.tick.percentage = 0.5,
      labels.niceFacing = FALSE)
  }
)

edit: added a note that axes widths should remain the same

user_3793666 · Answer

Something along these lines should work:

    # Libraries
library(tidyverse)
library(viridis)
library(patchwork)
library(hrbrthemes)
library(circlize)
library(chorddiag)  #devtools::install_github("mattflor/chorddiag")
# Load dataset from github
data <- read.table("https://raw.githubusercontent.com/holtzy/data_to_viz/master/Example_dataset/13_AdjacencyDirectedWeighted.csv", header=TRUE)

# short names
colnames(data) <- c("Africa", "East Asia", "Europe", "Latin Ame.",   "North Ame.",   "Oceania", "South Asia", "South East Asia", "Soviet Union", "West.Asia")
rownames(data) <- colnames(data)

# I need a long format
data_long <- data %>%
  rownames_to_column %>%
  gather(key = 'key', value = 'value', -rowname)

# parameters
circos.clear()
circos.par(start.degree = 90, gap.degree = 4, track.margin = c(-0.1, 0.1), points.overflow.warning = FALSE)
par(mar = rep(0, 4))

# color palette
mycolor <- viridis(10, alpha = 1, begin = 0, end = 1, option = "D")
mycolor <- mycolor[sample(1:10)]



# new code
mat <- as.matrix(data)
col_mat <- matrix("a", 10, 10)
for(i in 1:10){
  col_mat[i, ] <- mycolor[i]
}
diag(col_mat) = "#00000000"


# Base plot
chordDiagram(
  x = mat, 
  grid.col = mycolor,
  col = col_mat,
  transparency = 0.25,
  directional = 1,
  direction.type = c("arrows", "diffHeight"), 
  diffHeight  = -0.04,
  annotationTrack = "grid", 
  annotationTrackHeight = c(0.05, 0.1),
  link.arr.type = "big.arrow", 
  link.sort = TRUE, 
  link.largest.ontop = TRUE)

# Add text and axis
circos.trackPlotRegion(
  track.index = 1, 
  bg.border = NA, 
  panel.fun = function(x, y) {
    
    xlim = get.cell.meta.data("xlim")
    sector.index = get.cell.meta.data("sector.index")
    
    # Add names to the sector. 
    circos.text(
      x = mean(xlim), 
      y = 3.2, 
      labels = sector.index, 
      facing = "bending", 
      cex = 0.8
    )
    
    # Add graduation on axis
    circos.axis(
      h = "top", 
      major.at = seq(from = 0, to = xlim[2], by = ifelse(test = xlim[2]>10, yes = 2, no = 1)), 
      minor.ticks = 1, 
      major.tick.percentage = 0.5,
      labels.niceFacing = FALSE)
  }
)

Chord Diagram: hiding arrows directing to the same sector

1 Answers