Ternary plot with cummeRbund and ggplot2 (adapted from http://srmulcahy.github.io/2012/12/04/ternary-plots-r.html)

ternary.R

require(ggplot2)
require(grid)
require(scales)

ternary <- function(t, l, r, clr = clr, pts = pts, labels = c("top", "left", "right"), showGrid = TRUE){
    library(ggplot2)
    
    ddf <- data.frame(t, l, r)
    
    # convert points to cartesian coordinates
    ddf$y <- (10 / 100)* t * 0.86603
    ddf$x <- (ddf$y * 0.57735) + ((10 / 100) * r)
    ddf$clr <- clr
    ddf$pts <- pts
    
    # Find distance relative to each vertex
    vt<-c(5,8.66)
    vl<-c(0,0)
  	vr<-c(10,0)

  # border
    x1 <- c(0, 0 , 5)
  x2 <- c(10, 5, 10)
  y1 <- c(0, 0, 8.66)
  y2 <- c(0, 8.66, 0)
    bdf <- data.frame(x1, x2, y1, y2)
  
  # ternary grid
    x1 <- seq(1, 9, 1)
    x2 <- seq(0.5, 4.5, 0.5)
    x3 <- seq(5.5, 9.5, 0.5)
    x4 <- seq(4.5, 0.5, -0.5)
    y1 <- 0
  y2 <- seq(0.866, 7.794, 0.866)
    y3 <- seq(7.794, 0.866, -0.866)
    tdf <- data.frame(x1, x2, x3, x4, y1, y2, y3)
  
  #Axes

    # plot ternary diagram
  if(showGrid == TRUE){
    base <- ggplot(ddf) +
      # plot axis grid
      geom_segment(data = tdf, aes(x = x1, y = y1, xend = x2, yend = y2), 
                    linetype = "dashed", size = 0.25, colour = "grey50") +
      geom_segment(data = tdf, aes(x = x1, y = y1, xend = x3, yend = y3), 
                    linetype = "dashed", size = 0.25, colour = "grey50") +
      geom_segment(data = tdf, aes(x = x4, y = y3, xend = x3, yend = y3), 
                    linetype = "dashed", size = 0.25, colour = "grey50") +
      # plot border
      geom_segment(data = bdf, aes(x = x1, y = y1, xend = x2, yend = y2)) +
      # remove cartesian elements
      theme_bw() + 
      theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), 
            panel.border = element_blank(), axis.ticks = element_blank(), 
            axis.text.x = element_blank(), axis.text.y = element_blank(),
            axis.title.x = element_blank(), axis.title.y = element_blank()) +
      # add plot labels
      geom_text(aes(5, 9, label = labels[1]),data=data.frame()) +
      geom_text(aes(-1, 0, label = labels[2]),data=data.frame()) +
      geom_text(aes(11, 0, label = labels[3]),data=data.frame())
  } else {
    # if grid==FALSE don't plot grid
    base <- ggplot(ddf) +
      # plot border
      geom_segment(data = bdf, aes(x = x1, y = y1, xend = x2, yend = y2)) +
      # remove cartesian elements 
      theme_bw() +
      theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), 
            panel.border = element_blank(), axis.ticks = element_blank(), 
            axis.text.x = element_blank(), axis.text.y = element_blank(),
            axis.title.x = element_blank(), axis.title.y = element_blank()) +
      geom_text(aes(5, 9, label = labels[1])) +
      geom_text(aes(-1, 0, label = labels[2])) +
      geom_text(aes(11, 0, label = labels[3]))
  }
    
  # plot data on top of base plot
    p <- base +
        geom_point(data = ddf, aes(x = x, y = y, colour = clr, pch = pts), size = 1.5) +
        geom_point(x=5,y=3.5,color="black",size=2) +
        scale_colour_brewer(palette="Set1") +
        coord_equal(1)

    p
}

#Make Ternary plot
cuff<-readCufflinks()

myConditions<-c("A","B","C")

myGenes<-getGenes(cuff,myGeneIDs)

fpkmMat<-fpkmMatrix(myGenes)[,colnames(fpkmMatrix(myGenes)) %in% myConditions]
fpkmMat<-t(makeprobs(t(fpkmMat)))
fpkmMat<-fpkmMat*100
fpkmMat<-as.data.frame(fpkmMat)

labels<-myConditions

labels<-c("CP","VZ","SVZ_IZ")

p<-ternary(t=fpkmMat[[myConditions[1]]],l=fpkmMat[[myConditions[1]]],r=fpkmMat[[myConditions[1]]],labels=labels,clr="",pts="",showGrid=TRUE)
p