R/plot.statis.R

In ClustBlock: Clustering of Datasets

## =============================================================================


##' @title Display the STATIS charts
##' @usage
##' \method{plot}{statis}(x, axes=c(1,2), Graph_obj=TRUE,
##' Graph_weights=TRUE, Graph_eig=TRUE, tit="STATIS", col=NULL, cex=1, font=1,
##' xlim=NULL, ylim=NULL, ...)
##'
##' @description
##' This function plots the STATIS map and STATIS weights
##'
##'
##' @param x object of class 'statis'
##'
##' @param Graph_obj logical. Should the compromise graphical representation be plotted? Default: TRUE
##'
##' @param Graph_weights logical. Should the barplot of the weights be plotted? Default: TRUE
##'
##' @param Graph_eig logical. Should the barplot of the eigenvalues be plotted? Only with Graph_obj=TRUE. Default: TRUE
##'
##' @param axes  numerical vector (length 2). Axes to be plotted. Default: c(1,2)
##'
##' @param tit string. Title for the objects graphical representation. Default: 'STATIS'
##'
##' @param col vector. Color for each object. If NULL, col=rainbow(nrow(Data)). Default: NULL
##'
##' @param cex numerical. Numeric character expansion factor; multiplied by par("cex") yields the final character size. NULL and NA are equivalent to 1.0.
##'
##' @param font numerical. Integer specifying font to use for text. 1=plain, 2=bold, 3=italic, 4=bold italic, 5=symbol. Default: 1
##'
##' @param xlim numerical vector (length 2). Minimum and maximum for x coordinates.
##'
##' @param ylim numerical vector (length 2). Minimum and maximum for y coordinates.
##'
##' @param ... further arguments passed to or from other methods
##'
##'
##' @return the STATIS graphs
##'
##' @keywords quantitative
##'
##'
##' @examples
##' \donttest{
##'  data(smoo)
##'  NameBlocks=paste0("S",1:24)
##'  st=statis(Data=smoo,Blocks=rep(2,24),NameBlocks = NameBlocks)
##'  plot(st, axes=c(1,3), Graph_weights=FALSE)
##'
##'  }
##'
##' @seealso \code{\link{statis}}
##'
##' @export

## =============================================================================



plot.statis <- function(x, axes = c(1, 2), Graph_obj = TRUE, Graph_weights = TRUE, Graph_eig = TRUE,
                        tit = "STATIS", col = NULL, cex = 1, font = 1, xlim = NULL, ylim = NULL, ...) {
  res.statis <- x
  if (inherits(res.statis, "statis") == FALSE) {
    stop("The class of the object must be 'statis'")
  }

  if (Graph_obj == TRUE) {
    # show graphical representation
    C <- res.statis$coord
    if (is.null(col) == TRUE) {
      col <- rainbow(nrow(C))
    }
    vp <- res.statis$eigenvalues
    if (Graph_eig == TRUE) {
      dev.new()
      barplot(vp, col = "blue", main = "Eigenvalues")
    }
    pouriner <- res.statis$inertia
    un <- axes[1]
    deux <- axes[2]
    if (is.null(xlim) == TRUE) {
      xlim <- c(min(C[, un]) - 0.2, max(C[, un]) + 0.2)
    }
    if (is.null(ylim) == TRUE) {
      ylim <- c(min(C[, deux]) - 0.2, max(C[, deux]) + 0.2)
    }
    dev.new()
    plot(C[, un], C[, deux], type = "n", lwd = 5, pch = 16, xlab = paste("Dim", axes[1], "(", pouriner[un], "%)"), ylab = paste("Dim", axes[2], "(", pouriner[deux], "%)"), xlim = xlim, ylim = ylim)
    text(C[, un], C[, deux], rownames(C), col = col, cex = cex, font = font)
    abline(h = 0, v = 0)
    title(tit)


    # projection of each object of each block

    dev.new()
    n <- res.statis$param$n
    nblo <- res.statis$param$nblo
    configs <- res.statis$proj_config
    plot(C[, un], C[, deux], type = "n", lwd = 5, pch = 16, xlab = paste("Dim", axes[1], "(", pouriner[un], "%)"), ylab = paste("Dim", axes[2], "(", pouriner[deux], "%)"), xlim = c(min(C[, un]) - 0.25, max(C[, un]) + 0.25), ylim = c(min(C[, deux]) - 0.25, max(C[, deux]) + 0.25))
    text(C[, un], C[, deux], rownames(C), col = rainbow(n), font = 2)
    for (l in 1:nblo)
    {
      points(configs[, un, l], configs[, deux, l], col = rainbow(n), pch = 20)
      arrows(C[, un], C[, deux], configs[, un, l], configs[, deux, l], col = rainbow(n), lwd = 0.5, lty = 2, angle = 0)
    }
    abline(h = 0, v = 0)
    title(tit)
  }

  if (Graph_weights == TRUE) {
    dev.new()
    barplot(res.statis$weights)
    title(paste("Weights"))
  }
}