Which library could be used to make a Chord diagram in R? [closed]

Question

Is there any package in cran which could plot a chord layout like this: (this visualization is also called chord diagram)

Answer 1

I wrote the following several years ago, but never really used it: feel free to adapt it to your needs, or even turn it into a full-fledged package.

# Return a line in the Poincare disk, i.e., # a circle arc, perpendicular to the unit circle, through two given points. poincare_segment <- function(u1, u2, v1, v2) {     # Check that the points are sufficiently different     if( abs(u1-v1) < 1e-6 && abs(u2-v2) < 1e-6 )         return( list(x=c(u1,v1), y=c(u2,v2)) )     # Check that we are in the circle     stopifnot( u1^2 + u2^2 - 1 <= 1e-6 )     stopifnot( v1^2 + v2^2 - 1 <= 1e-6 )     # Check it is not a diameter     if( abs( u1*v2 - u2*v1 ) < 1e-6 )         return( list(x=c(u1,v1), y=c(u2,v2)) )     # Equation of the line: x^2 + y^2 + ax + by + 1 = 0 (circles orthogonal to the unit circle)     a <- ( u2 * (v1^2+v2^2) - v2 * (u1^2+u2^2) + u2 - v2 ) / ( u1*v2 - u2*v1 )     b <- ( u1 * (v1^2+v2^2) - v1 * (u1^2+u2^2) + u1 - v1 ) / ( u2*v1 - u1*v2 ) # Swap 1's and 2's     # Center and radius of the circle     cx <- -a/2     cy <- -b/2     radius <- sqrt( (a^2+b^2)/4 - 1 )     # Which portion of the circle should we draw?     theta1 <- atan2( u2-cy, u1-cx )     theta2 <- atan2( v2-cy, v1-cx )     if( theta2 - theta1 > pi )         theta2 <- theta2 - 2 * pi     else if( theta2 - theta1 < - pi )         theta2 <- theta2 + 2 * pi     theta <- seq( theta1, theta2, length=100 )     x <- cx + radius * cos( theta )     y <- cy + radius * sin( theta )     list( x=x, y=y ) }  # Sample data n <- 10 m <- 7 segment_weight <- abs(rnorm(n)) segment_weight <- segment_weight / sum(segment_weight) d <- matrix(abs(rnorm(n*n)),nr=n, nc=n) diag(d) <- 0 # No loops allowed # The weighted graph comes from two quantitative variables d[1:m,1:m] <- 0 d[(m+1):n,(m+1):n] <- 0 ribbon_weight <- t(d) / apply(d,2,sum) # The sum of each row is 1; use as ribbon_weight[from,to] ribbon_order <- t(apply(d,2,function(...)sample(1:n))) # Each row contains sample(1:n); use as ribbon_order[from,i] segment_colour <- rainbow(n) segment_colour <- brewer.pal(n,"Set3") transparent_segment_colour <- rgb(t(col2rgb(segment_colour)/255),alpha=.5) ribbon_colour <- matrix(rainbow(n*n), nr=n, nc=n) # Not used, actually... ribbon_colour[1:m,(m+1):n] <- transparent_segment_colour[1:m] ribbon_colour[(m+1):n,1:m] <- t(ribbon_colour[1:m,(m+1):n])  # Plot gap <- .01 x <- c( segment_weight[1:m], gap, segment_weight[(m+1):n], gap ) x <- x / sum(x) x <- cumsum(x) segment_start <- c(0,x[1:m-1],x[(m+1):n]) segment_end   <- c(x[1:m],x[(m+2):(n+1)]) start1 <- start2 <- end1 <- end2 <- ifelse(is.na(ribbon_weight),NA,NA) x <- 0 for (from in 1:n) {   x <- segment_start[from]   for (i in 1:n) {     to <- ribbon_order[from,i]     y <- x + ribbon_weight[from,to] * ( segment_end[from] - segment_start[from] )     if( from < to ) {       start1[from,to] <- x       start2[from,to] <- y     } else if( from > to ) {       end1[to,from] <- x       end2[to,from] <- y     } else {       # no loops allowed     }     x <- y   } }  par(mar=c(1,1,2,1)) plot(   0,0,    xlim=c(-1,1),ylim=c(-1,1), type="n", axes=FALSE,    main="Two qualitative variables in polar coordinates", xlab="", ylab="") for(from in 1:n) {   for(to in 1:n) {     if(from<to) {       u <- start1[from,to]       v <- start2[from,to]       x <- end1  [from,to]       y <- end2  [from,to]       if(!is.na(u*v*x*y)) {             r1 <- poincare_segment( cos(2*pi*v), sin(2*pi*v), cos(2*pi*x), sin(2*pi*x) )             r2 <- poincare_segment( cos(2*pi*y), sin(2*pi*y), cos(2*pi*u), sin(2*pi*u) )             th1 <- 2*pi*seq(u,v,length=20)             th2 <- 2*pi*seq(x,y,length=20)             polygon(                 c( cos(th1), r1$x, rev(cos(th2)), r2$x ),                 c( sin(th1), r1$y, rev(sin(th2)), r2$y ),                 col=transparent_segment_colour[from], border=NA             )       }     }   } } for(i in 1:n) {   theta <- 2*pi*seq(segment_start[i], segment_end[i], length=100)   r1 <- 1   r2 <- 1.05   polygon(      c( r1*cos(theta), rev(r2*cos(theta)) ),     c( r1*sin(theta), rev(r2*sin(theta)) ),     col=segment_colour[i], border="black"   ) } 

Answer 2

The chorddiag package (still in development) provides an interactive D3 implementation

The chorddiag package allows to create interactive chord diagrams using the JavaScript visualization library D3 (http://d3js.org) from within R using the htmlwidgets interfacing framework..

Example

devtools::install_github("mattflor/chorddiag") library(chorddiag)  ## example taken from the github site m <- matrix(c(11975,  5871, 8916, 2868,               1951, 10048, 2060, 6171,               8010, 16145, 8090, 8045,               1013,   990,  940, 6907),             byrow = TRUE,             nrow = 4, ncol = 4) haircolors <- c("black", "blonde", "brown", "red") dimnames(m) <- list(have = haircolors,                     prefer = haircolors) m #             prefer #   have     black blonde brown  red #     black  11975   5871  8916 2868 #     blonde  1951  10048  2060 6171 #     brown   8010  16145  8090 8045 #     red     1013    990   940 6907  groupColors <- c("#000000", "#FFDD89", "#957244", "#F26223") chorddiag(m, groupColors = groupColors, groupnamePadding = 40)