R/plot_vp_euler3.R

In jgmv/comecol: Community Ecology Analysis

#' Plot Euler Diagram From Variation Partition Results (3 Vars)
#'
#' Plots an Euler diagram from an object created with vegan's 'varpart' function, using three explanatory variables.
#' @param vp output from 'varpart' analysis.
#' @param names vector with the names of the tables with explanatory variables.
#' @param color vector with colors for the diagram bubbles.
#' @return An Euler plot.
#' @keywords community data
#' @export
#' @examples
#' plot_vp_euler3()
plot_vp_euler3 <- function(vp, names = c("X1", "X2", "X3"),
  col = c("brown3", "skyblue3", "orange")) {
  require(venneuler)
  sec <- vp$part$indfract[-8, 3]
  sec <- ifelse(sec < 0, 0, sec)
  res <- vp$part$indfract[8, 3]
  names(sec)<- c(names, paste(names[1], names[2], sep = "&"),
    paste(names[2], names[3], sep = "&"), paste(names[1], names[3], sep = "&"),
    paste(names[1], names[2], names[3], sep = "&"))
  vd <- venneuler::venneuler(sec, residuals = res)
  plot(vd, col = col)
  mtext(paste("Residuals = ", round(res, 2), sep = ""), 1, cex = 1)
}