R/themes.R

In kmiddleton/abd: The Analysis of Biological Data

#' Lattice theme for Analysis of Biological Data
#'
#' This theme will help produce plots with color scheme similar to the one used
#' in \emph{Analysis of Biological Data}
#'
#'
#' @rdname themes
#' @param bw a logical. Use a grayscale theme instead of color?
#' @param lty line types used for \code{panel.superpose}
#' @return a list that can be used as a \code{lattice} theme.
#' @details
#' \code{theme.abd} and \code{col.abd} are the same function with
#' two names.
#' @author Randall Pruim (\email{rpruim@@calvin.edu})
#' @keywords graphics
#' @aliases col.abd,theme.abd
#' @export
#' @examples
#'
#' trellis.par.set(theme=col.abd(bw=TRUE))
#' show.settings()
#' trellis.par.set(theme=theme.abd(lty=1))
#' show.settings()
#'
col.abd <- function (bw = FALSE, lty = 1:7) {
  aRed <- colorRampPalette(c("white", "darkred"))(10)[10]
  paleRed <- colorRampPalette(c("white", "darkred"))(10)[4]
  lightBlue <- colorRampPalette(c("white", "steelblue"))(10)[5]
  lightRed <- colorRampPalette(c("white", "darkred"))(10)[6]
  veryLightRed <- colorRampPalette(c("white", "darkred"))(12)[3]
  paleGreen <- colorRampPalette(c("white", "darkGreen"))(10)[8]
  if (bw) {
      return(list(
    background = list(col = "transparent"),
    axis.line = list(col = "gray30"),
          axis.text = list(col = "gray30"),
    plot.polygon = list(col = "gray80"),
          box.rectangle = list(col = "gray10"),
    box.umbrella = list(col = "gray10", lty = 1),
    box.dot = list(col = "gray10"),
    dot.line = list(col = "gray50"),
          dot.symbol = list(col = "gray30", pch = 16),
    plot.line = list(col = "black", lwd = 2),
    plot.symbol = list(col = "black", fill = "gray80", pch = 16),
    regions = list(col = gray((1:100)/100)),
          reference.line = list(col = "gray50"), add.line = list(lty = 1, col = "gray80", lwd = 2),
    superpose.polygon = list(col = c("gray30", "gray70", "black", "gray50", "gray20",
      "gray80", "gray60", "gray40"),
    fill = c("gray80")),
    superpose.line = list(lty = lty, lwd = 2,
      col = c("gray30", "gray70", "black", "gray50", "gray20", "gray80", "gray60", "gray40")),
          superpose.symbol = list(
      pch = c(16, 15, 18, 1, 3, 6, 0, 5),
      cex = rep(0.7, 7),
      col = c("gray30", "gray70", "black", "gray50", "gray20", "gray80", "gray60", "gray40")),
    strip.background = list(alpha = 1, col = c("gray80", "gray65")),
    strip.shingle = list(alpha = 1, col = c("gray60", "gray30")),
    par.strip.text = list(cex = 0.5)
    ))
  }
  else {
      return(list(
    background = list(col = "transparent"),
    plot.polygon = list(col = "darkred"),
          box.rectangle = list(col = "darkred"),
    box.umbrella = list(col = "darkred"),
          dot.line = list(col = "#e8e8e8"),
    dot.symbol = list(col = "darkred", pch = 16),
    plot.line = list(lwd = 2, col = 'darkred'),
    plot.symbol = list(col = "darkred", pch = 16),
    # regions = list(col = heat.colors(100)),
      regions = list(col= colorRampPalette(c("red", "darkorange", "orange", "yellow", "white"))(100)),
          reference.line = list(col = "#e8e8e8"),
    add.line = list(lty = 1, col = "gray20", lwd = 2),
    superpose.polygon = list(
      col = c("darkred", "orange","lightskyblue3", "darkgreen", "darkorchid4", "pink", "lightgreen")
      ),
    superpose.line = list(lty = lty, lwd = 2,
      col = c("darkred", "orange", "navy", "darkgreen", "lightskyblue3", "darkorchid4", "pink", "lightgreen")
      ),
          superpose.symbol = list(
      pch = c(16, 15, 18, 1, 3, 6, 0, 5),
      cex = rep(0.7, 7),
      col = c("darkred", "orange", "navy", "darkgreen", "lightskyblue3", "darkorchid4", "pink", "lightgreen")
      ),
    strip.background = list(alpha = 1,
      col = c(veryLightRed, "#ffe5cc", "#cce6ff", "#ccffff", "#ffccff", "#ffcccc", "#ffffcc")
      ),
          strip.shingle = list(alpha = 1,
      col = c(lightRed,"#ff7f00", "#0080ff", "#00ffff", "#ff00ff", "#ff0000", "#ffff00")),
      par.strip.text = list(cex = 0.5)
    ))
  }
}

#' @rdname themes
#' @export
theme.abd <- col.abd