Plotting a kde result in ggtern

Question

I'm using ggtern to plot a large dataset in a form of tertiary plot (see below an example).

Till a certain data-size everything was perfect, as I was using geom_density_tern(). As I want to visualize a far more complicated dataset loading all of it and rendering with ggplot becomes impossible (limitation on the memory side). I thought that maybe there could be a workaround by imputing the result of kde2d matrix calculated seperately. And that's where I'm stuck. I would like to know if it is possible to do it anyhow in ggtern?

In any case I add a minimal case of the data structure and plotting that I use at this moment.

require(ggplot2)
require(ggtern) 

set.seed(1) 

mydata <- data.frame(
        x = runif(100, min = 0.25, max = 0.5),
        y = runif(100, min = 0.1, max = 0.4),
        z = runif(100, min = 0.5, max = 0.7))   

plot <- ggtern() + 
        theme_bw() +
        theme_hidetitles() +
        geom_density_tern(data = mydata,
            aes(x = x, y = y, z = z, alpha = ..level.. ), 
            size = 0.1, linetype = "solid", fill = "blue")+
        geom_point(data = mydata, 
            aes(x = x, y = y, z = z), alpha = 0.8, size = 1)
plot

Those extra lines reproduce the density plot in the ternary coordination system:

library(MASS)
dataTern = transform_tern_to_cart(mydata$x,mydata$y,mydata$z)
dataTernDensity <- kde2d(x=dataTern$x, y=dataTern$y, lims = c(range(0,1), range(0,1)), n = 400) 

image(dataTernDensity$x, dataTernDensity$y, dataTernDensity$z)
points(dataTern$x, dataTern$y, pch = 20, cex = 0.1)
segments(x0 = 0, y0 = 0, x1 = 0.5, y1 = 1, col= "white")
segments(x0 = 0, y0 = 0, x1 = 1, y1 = 0, col= "white")
segments(x0 = 0.5, y0 = 1, x1 = 1, y1 = 0, col= "white")

And obtaining this graph:

Thanks in advance for any help!

Do I understand correctly that you can call `kde2`, but out of memory for `ggtern + geom_density_tern`? — tonytonov, Jan 15 '16 at 16:15
I meant that in my "real" analysis I have a huge data frame, that is far to big for the geom_density_tern to handle in one go. I thought to load in geom_density_tern a precalculated kde2 matrix. Is it more understandable? — Ludwik, Jan 15 '16 at 17:05

score 2 · Accepted Answer · edited Jan 18 '16 at 10:58

We can solve this using the code which is usually used behind the scenes in the Stat. Having just released ggtern 2.0.1, published on CRAN a couple of days ago after completely re-writing the package to be compatible with ggplot2 2.0.0, I am familiar with an approach that may suit your needs. Incidentally, for you interest, a summary of the new functionality in ggtern 2.0.X can be found here:

Below please find a solution and working code for your problem, which is a density estimate calculated on isometric log-ratio space.

#Required Libraries
library(ggtern)
library(ggplot2)
library(compositions)
library(MASS)
library(scales)

set.seed(1) #For Reproduceability
mydata <- data.frame(
  x = runif(100, min = 0.25, max = 0.5),
  y = runif(100, min = 0.1, max = 0.4),
  z = runif(100, min = 0.5, max = 0.7)) 

#VARIABLES
nlevels  = 7
npoints  = 200
expand   = 0.5

#Prepare the data, put on isometric logratio basis
df     = data.frame(acomp(mydata)); colnames(df) = colnames(mydata)
data   = data.frame(ilr(df)); colnames(data) = c('x','y')

#Prepare the Density Estimate Data
h.est  = c(MASS::bandwidth.nrd(data$x), MASS::bandwidth.nrd(data$y))
lims   = c(expand_range(range(data$x),expand),expand_range(range(data$y),expand))
dens   = MASS::kde2d(data$x,data$y,h=h.est,n=npoints,lims=lims)

#-------------------------------------------------------------
#<<<<< Presumably OP has data at this point, 
#      and so the following should achieve solution
#-------------------------------------------------------------

#Generate the contours via ggplot2's non-exported function
lines  = ggplot2:::contour_lines(data.frame(expand.grid(x = dens$x, y = dens$y),
                                            z=as.vector(dens$z),group=1),
                                 breaks=pretty(dens$z,n=nlevels))

#Transform back to ternary space
lines[,names(mydata)] = data.frame(ilrInv(lines[,names(data)]))

#Render the plot
ggtern(data=lines,aes(x,y,z)) +
  theme_dark() + 
  theme_legend_position('topleft') + 
  geom_polygon(aes(group=group,fill=level),colour='grey50') +
  scale_fill_gradient(low='green',high='red') + 
  labs(fill  = "Density",
       title = "Example Manual Contours from Density Estimate Data")

Thanks for this solution. I added library(scales) line, as without it the expand_range() function was missing. — Ludwik, Jan 18 '16 at 10:32
There is still an issue with plotting the data, but for that I'll open a new thread. — Ludwik, Jan 18 '16 at 10:37
Sorry, forgot to include scales, I had it loaded from something else. What is the additional issue? — Nicholas Hamilton, Jan 18 '16 at 10:58

Plotting a kde result in ggtern

1 Answers1