link.arr.col not working with dataframe (bug?)

[cardosan]

as example if I try to use link.arr.col just get white arrows for all the links using the tutorial as MWE (tried also in my own data with a dataframe passed with same results) :

library(circlize)
# library(gtools)
# library(dplyr)

set.seed(999)
mat = matrix(sample(18, 18), 3, 6)
rownames(mat) = paste0("S", 1:3)
colnames(mat) = paste0("E", 1:6)
mat

df = data.frame(from = rep(rownames(mat), times = ncol(mat)),
                to = rep(colnames(mat), each = nrow(mat)),
                value = as.vector(mat),
                stringsAsFactors = FALSE)
grid.col = c(S1 = "red", S2 = "green", S3 = "blue",
             E1 = "grey", E2 = "grey", E3 = "grey", E4 = "grey", E5 = "grey", E6 = "grey")

# 
lty_df = data.frame(c("S1", "S2", "S3"), c("E5", "E6", "E4"), c(1, 2, 3))
lwd_df = data.frame(c("S1", "S2", "S3"), c("E5", "E6", "E4"), c(2, 2, 2))
border_df = data.frame(c("S1", "S2", "S3"), c("E5", "E6", "E4"), c(1, 1, 1))
arr.col = data.frame(c("S1", "S2", "S3"), c("E5", "E6", "E4"),
                     c("black", "black", "black"))
# 
chordDiagram(df,
#              # reduce=0,
             # grid.col = grid.col,
             # link.lty = lty_df,
             # link.lwd = lwd_df,
             directional = 2,
             direction.type = c("diffHeight", "arrows"),
             link.arr.col = arr.col,
            #   link.arr.length = 0.2,
            # link.border = border_df
             )

circos.clear()

I also get some 50 warnings like:

Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
  supplied color is neither numeric nor character

Is it a bug or am I wrong in something?

[jokergoo]

Hi, the support for link.arr.col as a data frame is missing. I only considered it when the first argument is a matrix while I totally forgot to test it when the first argument is a data frame.

Currently, you can set link.arr.col as a color vector which has the same order as df. link.arr.col as a data frame will be supported very soon.

chordDiagram(df,
             directional = 2,
             direction.type = c("diffHeight", "arrows"),
             link.arr.col = c("black", rep("white", nrow(df) - 1))
             )

[jokergoo]

Hi, I have updated the package, now link.arr.col as data frame is supported now.

[cardosan]

indeed it works now, thanks!

[akkalbist55]

Hi, jokergoo this is my code and there is some problem in fill "follow" in boundary also mow to represent season in separate network flowing line please help me!!

library(circlize)

export_dist <- c("Kailali","Kathmandu","Bardia","Kathmandu","Bardia","Kathmandu","Dolakha","Bajhang","Kailali","Kailali","Bardia","Sagaematha","Kailali","Kathmandu","Kathmandu","Kathmandu","Bardia","Mahendranagar","Bardia","Sanja","Salleri","Jajarkot","Bajura")
import_dist <- c("Butwal","Bardia","Sagarmatha","Butwal","Bajhang","Bajhang","Lalitpur","Kathmandu","Lalitpur","Lalitpur","Mahendranagar","Kailali","Butwal","Kathmandu","Dolakha","Butwal","Lalitpur","Butwal","Lalitpur","Lalitpur","Vojpur","Vojpur","Dolakha")
flow <- c(2000,65780,78010,851,35353,845,738,120788,245900,90002,4426,6870,152681,78114,32591,19274,10915,23100,6275,4544,8750,9800,1349)
season<- c("Spring","Summer","Winter","Autumn","Summer","Winter","Autumn","Spring","Summer","Winter","Autumn","Summer","Winter","Autumn","Summer","Winter","Autumn","Summer","Winter","Autumn","Spring","Summer","Winter")
df <- data.frame(export_dist, import_dist, flow,stringsAsFactors = FALSE)

dist = unique(c(df[[1]], df[[2]]))
color <- c("#E41A1C","#800000","#ff8c00","#ffd700","#008000","#00bfff","#377EB8",
           "#ff69b4","#800080","#4b0082","#000000","#800000","#E8ECE7","#7109D3","#5F4974")

df1 <- data.frame(dist, color,stringsAsFactors = FALSE)

circos.clear()
circos.par(start.degree = 90, gap.degree = 5, track.margin = c(-0.1, 0.1), points.overflow.warning = FALSE)
par(mar = rep(0, 4))

chordDiagram(x = df[1:2],log10(df[3]), grid.col = color, transparency = 0.25,
             order = dist, directional = 1,
             direction.type = c("arrows", "diffHeight"), diffHeight  = -0.04,
             annotationTrack = c("grid","axis"), annotationTrackHeight = c(0.05, 0.1),
             link.arr.type = "big.arrow", link.sort = TRUE, link.largest.ontop = TRUE)

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")
    dist = df1$dist[df1$dist == sector.index]

    circos.text(x = mean(xlim), y = 4.4, 
                labels = dist, facing = "bending", cex = 1, niceFacing = TRUE, adj = c(0.5, 0))

  }
)

for(i in seq_len(nrow(res))) {
  circos.text(x = res$x1[i] - res$value[i]/2, y = 0.5, round(10^(res$value[i])), facing = "inside",
              niceFacing = TRUE, adj = c(0.5, 0.5), cex = 0.5, col = "white", sector.index = res$rn[i], track.index = 1)
  circos.text(x = res$x2[i] - res$value[i]/2, y = 0.5, round(10^(res$value[i])), facing = "inside",
              niceFacing = TRUE, adj = c(0.5, 0.5), cex = 0.5, col = "white", sector.index = res$cn[i], track.index = 1)
}

[akkalbist55]

this is look like