R/plot_obspc.R

In fhernanb/model: This Package Contains Useful Functions for Modeling Regresion

#' Plot observations in the coordinate plane PC1-PC2.
#' 
#' This function plots the observations in the coordinate plane PC1-PC2.
#' 
#' @param mod a prcomp or princomp object obtained from \code{\link{prcomp}} or \code{\link{princomp}} functions.
#' @param lchar the number of first characters to identify points.
#' @param pch  an integer specifying a symbol or a single character to be used as the default in plotting points.
#' @param ... arguments to be passed to methods, such as graphical parameters (see par).
#' 
#' @example examples/examples_plot_obspc.R
#' @return The function returns a list with two elements, coordinate points for first
#' and second dimensions.
#' 
#' @importFrom graphics plot points text abline
#' @export
plot_obspc <- function(mod, lchar=3, pch=20, ...) {
  stopifnot(class(mod) %in% c('prcomp', 'princomp'))
  if (inherits(mod, "prcomp")) {
    scores <- mod$x
  } else {
    scores <- mod$scores
  }
  if (is.null(rownames(scores))) {
    n <- dim(scores)[1]
    rownames(scores) <- 1:n
    lchar <- nchar(n)
  }
  Names <- substr(rownames(scores), start=1, stop=lchar)
  plot(scores[, 1:2], type='n', las=1, ...)
  points(scores[, 1:2], pch=pch, ...)
  text(scores[, 1:2], labels=Names, adj=c(0, 0))
  abline(h=0, col="gray60", lty='longdash')
  abline(v=0, col="gray60", lty='longdash')
}