Visualize poppr population hierarchies with treemap

poppr_treemap.R

#==============================================================================#
# Visualize the population hierarchy of a genclone object.
#
# Packages needed (install beforehand):
library(poppr)
library(treemap)
#==============================================================================#
# Main function
# 
# Inputs:
#   x - a genclone object
#   h - a hierarchical formula (see examples below)
#   show - if TRUE, the plot will be displayed, if FALSE, the data necessary
#          to create the plot will be displayed.
#   ... - any arguments passed on to the treemap function.
make_treemap <- function(x, h = NULL, show = TRUE, ...){
  if (is.null(h)){
    hier <- unique(strata(x))
  } else {
    hier <- unique(strata(x, h, combine = FALSE))
  }
  form       <- make_formula(names(hier))
  setPop(x)  <- form
  hier$Count <- table(pop(x))
  if (show){
    return(treemap(hier, all.vars(form), "Count", ...))
  } else {
    return(c(list(dtf = hier, index = all.vars(form), vSize = "Count"), ...))
  }
}

make_formula <- function(x){
  if (is.language(x)){
    return(x)
  } else {
    return(as.formula(paste0("~", paste(x, collapse = "/")), env = .GlobalEnv))
  }
}

#==============================================================================#
# EXAMPLES
#==============================================================================#
# Using P. infestans data
data(Pinf)
make_treemap(Pinf, title = "P. infestans")
make_treemap(Pinf, ~Country, title = "P. infestans")

# Using A. euteiches data
data(Aeut)
strata(Aeut) <- other(Aeut)$population_hierarchy[-1]
make_treemap(Aeut, ~Pop/Subpop, vColor = "Pop", type = "categorical", title = "A. euteiches")

# Using M. fructicola data 
data(monpop)
splitStrata(monpop) <- ~Tree/Year/Symptom

# Don't show the plot and pass it to do.call
trees <- make_treemap(monpop, type = "categorical", vColor = "Tree", show = FALSE, title = "M. fructicola")
names(trees)
head(trees$dtf)
do.call("treemap", trees)

# here's a better plot without the tree labels. 
make_treemap(monpop, type = "categorical", vColor = "Tree", title = "M. fructicola", 
             align.labels = list(c("center", "top"), c("center", "center"), c("center", "bottom")), 
             fontsize.labels = c(0, 15, 15))

To run use:

# If you don't have these packages:
install.packages("treemap")
install.packages("poppr")

devtools::source_gist("91686d5d5d0bb2f14a38")