R/corrplot.mixed.R

In corrplot: Visualization of a Correlation Matrix

#' Using mixed methods to visualize a correlation matrix.
#'
#' @param corr Matrix, the correlation matrix to visualize.
#' @param lower Character, the visualization method for the lower triangular
#'   correlation matrix.
#' @param upper Character, the visualization method for the upper triangular
#'   correlation matrix.
#' @param tl.pos Character, \code{'lt'}, \code{'d'} or \code{'n'}, giving
#'   position of text labels, \code{'lt'} means left and top,  \code{'d'} means
#'   diagonal. If \code{'n'},  add no textlabel.
#' @param diag Character, for specifying the glyph on the principal diagonal. It
#'   is one of \code{'n'} (default,  draw nothing), \code{'l'} (draw the glyphs
#'   of lower triangular) or \code{'u'} (draw the glyphs of upper triangular).
#' @param bg The background color.
#' @param addgrid.col See the \code{addgrid.col} parameter in the function
#'   \code{\link{corrplot}}
#' @param lower.col Passed as \code{col} parameter to the lower matrix.
#' @param upper.col Passed as \code{col} parameter to the upper matrix.
#' @param plotCI See the \code{plotCI} parameter in the function
#'   \code{\link{corrplot}}
#' @param mar See \code{\link{par}}.
#' @param \dots Additional arguments for corrplot's wrappers
#'
#' @author Taiyun Wei
#' @example vignettes/example-corrplot.mixed.R
#' @export
corrplot.mixed = function(
  corr,
  lower = 'number',
  upper = 'circle',
  tl.pos = c('d', 'lt', 'n'),
  diag = c('n', 'l', 'u'),
  bg = 'white',
  addgrid.col = 'grey',
  lower.col = NULL,
  upper.col = NULL,
  plotCI = c('n', 'square', 'circle', 'rect'),
  mar = c(0, 0, 0, 0),
  ...)
{

  tl.pos = match.arg(tl.pos)
  diag = match.arg(diag)
  plotCI = match.arg(plotCI)
  n = nrow(corr)

  # fixes issue #21
  # some methods are not compatible with plotCI='rect'
  adjust_plotCI = function(plotCI, method) {
    if (plotCI != 'rect' || method %in% c('circle', 'square')) {
      return(plotCI)
    }
    return('n')
  }

  plotCI_lower = adjust_plotCI(plotCI, lower)
  plotCI_upper = adjust_plotCI(plotCI, upper)

  # fixed issue #102
  # restore this parameter when exiting the corrplot.mixed function in any way
  oldpar = par(mar = mar, bg = par()$bg)
  on.exit(par(oldpar), add = TRUE)

  corrplot(corr, type = 'upper', method = upper, diag = TRUE,
           tl.pos = tl.pos, plotCI = plotCI_upper,
           bg = bg, addgrid.col = addgrid.col,
           col = upper.col, mar = mar, ...) -> res1

  corrplot(corr, add = TRUE, type = 'lower', method = lower,
           diag = (diag == 'l'),
           bg = bg, addgrid.col = addgrid.col,
           tl.pos = 'n', cl.pos = 'n', plotCI = plotCI_lower,
           col = lower.col, mar = mar, ...) -> res2

  if (diag == 'n' && tl.pos != 'd') {
    # draw empty rectangles over the diagonal to 'clean' it graphically
    symbols(1:n, n:1, add = TRUE, bg = bg, fg = addgrid.col,
            inches = FALSE, squares = rep(1, n))
  }

  corr = res1$corr
  corrPos = rbind(res1$corrPos, res2$corrPos)
  corrPos = corrPos[order(corrPos[, 1], corrPos[, 2]), ]


  res = list(corr=corr, corrPos=corrPos)

  invisible(res)
}