R/plots.R

In CongreveLamsdell2016: Distance Metrics for Trees Generated by Congreve and Lamsdell

#' Initialize ternary plots for quartet plotting
#'
#' Sets up a blank ternary plot ready for analytical results to be added.
#'
#' @param gridCol Colour, passed to `TernaryPlot` as `grid.col`.
#' @param backgroundCol Background colour, passed to `TernaryPlot` as `col`.
#' @param gridLines Number of grid lines, passed to `TernaryPlot` as `grid.lines`.
#' @param xLim,yLim x and y limits, passed to `TernaryPlot` as `xlim`, `ylim`.
#' @param isometric Logical specifying whether plot should be isometric, passed
#' to `TernaryPlot` as `isometric`.
#' @param fontSize Font size, passed to `TernaryPlot` as `lab.cex`.
#' @param padding Padding, passed to `TernaryPlot`.
#' @param zoom Level of magnification (times), used to adjust ticks and scale.
#'
#' @importFrom Ternary TernaryPlot HorizontalGrid AddToTernary
#' @importFrom graphics lines
#'
#' @export
clInitializeTernaryQuarts <- function (zoom = 1, padding = 0.1, gridLines = 10,
                                       fontSize = 1,
                                       gridCol = "#DBDBDB",
                                       backgroundCol = "#FDFDFE",
                                       xLim = c(0, 1 / zoom) - 0.01,
                                       yLim = c(0.5-(1 / zoom), 0.5),
                                       isometric = TRUE
                                       ) {
  lab <- if (zoom == 1) c("unresolved quartets",
                          "different quartets",
                          "identical quartets") else rep("", 3)

  TernaryPlot(atip = NULL, btip = NULL, ctip = NULL,
              alab = lab[1], blab = lab[2], clab = lab[3],
              lab.cex = fontSize,
              lab.offset = 0.18, # higher value as longer tick labels
              point = "right", isometric = isometric,
              col = backgroundCol,
              grid.lty = "solid", grid.col = gridCol, grid.lines = gridLines,
              grid.minor.lines = 0,
              axis.labels = if(zoom == 1) {
                round(seq(0, choose(22, 4), length.out = 20), 0)
              } else if (zoom == 3.5) {
                round(seq(0, choose(22, 4), length.out = 20), 0)
              }
              else FALSE,
              axis.col = "#999999",
              axis.cex = fontSize,
              ticks.length = if (zoom == 1) 0.025 else 0.009,
              padding = padding, xlim = xLim, ylim = yLim)
  HorizontalGrid(gridLines)
  #SymmetricDifferenceLines(seq(0.1, 0.9, by = 0.1), col = "#888888",
  #                         lty = "dotted")
  AddToTernary(lines, list(c(0, 2/3, 1/3), c(1, 0, 0)), lty = "dotted",
               col = Ternary::cbPalette8[8], lwd = 2)
}

#' @describeIn clInitializeTernaryQuarts Initialize ternary plots for
#' partition plotting.
#' @export
clInitializeTernarySplits <- function(fontSize = 1, xLim = NULL, yLim = NULL,
                                      gridCol = "#DBDBDB",
                                      backgroundCol = "#FDFDFE",
                                      padding = 0.1, isometric = TRUE) {
  TernaryPlot(NULL, NULL, NULL,
              alab = "unresolved partitions",
              blab = "different partitions",
              clab = "identical partitions",
              lab.cex = fontSize, lab.offset = 0.16,
              col = backgroundCol, point = "right",
              grid.lines = 19, grid.lty = "solid", grid.col = gridCol,
              grid.minor.lines = 0,
              axis.col = "#999999",
              axis.cex = fontSize,
              padding = padding, axis.labels = 0:19,
              xlim = xLim, ylim = yLim, isometric = isometric)
  HorizontalGrid(grid.lines = 19)
}