ggplot2 approach to plotting the results of the candisc function found in the candisc package with 95% confidence ellipses. Needs editing to be completely compatible with candisc.

gg_candisc_plot.R

gg.candisc.plot <- function(candisc.object){


# Plot with ellipses using ggplot2 ####
require(grid)
require(ggplot2)
require(devtools)
require(digest)
#For info : http://stackoverflow.com/questions/2397097/how-can-a-data-ellipse-be-superimposed-on-a-ggplot2-scatterplot
source_url("https://raw.github.com/low-decarie/FAAV/master/r/stat-ellipse.R") 

#Nicer theme
theme_set(theme_bw())

#Basic score plot
labels <- names(candisc.object$scores)[1]
can.plot <- qplot(data=candisc.object$scores,
                   x=Can1,
                   y=Can2,
                   colour=get(labels))+
  stat_ellipse()+  #Add ellipses
  coord_equal()


#Add arrows

#Create arrow coordinates
arrow.coord <- data.frame(x=0,y=0,
                          xend=candisc.object$structure[,1],yend=candisc.object$structure[,2],
                          variable=row.names(candisc.object$structure))

#Enlarge arrows
enlarge <- 3
arrow.coord$xend <- enlarge*arrow.coord$xend
arrow.coord$yend <- enlarge*arrow.coord$yend


#Plot arrows
can.plot <- can.plot+geom_segment(data=arrow.coord,
                                    colour=I("black"),
                                    aes(x=x,
                                        y=y,
                                        xend=xend,
                                        yend=yend),
                                    arrow = arrow(length = unit(0.5,"cm")))

#Add arrow labels
can.plot <- can.plot+geom_text(data=arrow.coord,
                                 colour=I("black"),
                                 aes(x=xend,
                                     y=yend,
                                     label=variable,
                                     hjust=0.5,
                                     vjust=0.5))



print(can.plot)
}