R/colorscale.R

In pmpsa-hpc/NPA: Network Perturbation Amplitude

#####################################################################
## Copyright 2018 Philip Morris Products, S.A.
## Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
#####################################################################

#' Creates a color scale.
#'
#' @param x A \code{vector of numeric} of the data values.
#' @param col1 Color 1
#' @param col2 Color 2
#' @param col3 Color 3
#' @param col4 Color 4
#' @param col5 Color 5
#' @param signed A \code{logical} that specifies whether a symmetric color scale should be created.
#' @param minx Minimum value.
#' @param maxx Maximum value.
#'
#' @return A vector of colors.
colorscale <-
  function(x,
           col1 = "navy",
           col2 = "blue",
           col3 = "white",
           col4 = "orange",
           col5 = "red3",
           signed = FALSE,
           minx = min(x, na.rm = TRUE),
           maxx = max(x, na.rm = TRUE)) {
    if (length(col1) == 5) {
      col2 <- col1[2]
      col3 <- col1[3]
      col4 <- col1[4]
      col5 <- col1[5]
      col1 <- col1[1]
    }
    # if (signed == TRUE & (min(x, na.rm = TRUE) > 0 | max(x, na.rm = TRUE) < 0)) {
    # warning("No real signed version possible")
    # }
    if (signed == TRUE) {
      cole <- rep(NA, length(x))
      if (length(cole[x < 0 & !is.na(x)]) > 0) {
        cole[x < 0 &
               !is.na(x)] <- colorscale0(
                 c(x[x < 0 & !is.na(x)], 0),
                 col1,
                 col2,
                 col3,
                 col4 = NULL,
                 col5 = NULL,
                 minx = minx,
                 maxx = 0
               )[-length(c(x[x <
                               0 & !is.na(x)], 0))]
      }
      if (length(cole[x >= 0 & !is.na(x)]) > 0) {
        cole[x >= 0 & !is.na(x)] <- colorscale0(
          c(0, x[x >= 0 & !is.na(x)]),
          col3,
          col4,
          col5,
          col4 = NULL,
          col5 = NULL,
          minx = 0,
          maxx = maxx
        )[-1]
      }
    }
    if (signed == FALSE) {
      cole <-
        colorscale0(x,
                    col1,
                    col2,
                    col3,
                    col4,
                    col5,
                    minx = minx,
                    maxx = maxx)
    }
    return(cole)
  }

#' Generate color panels by using 5 colors.
#' @param n An \code{integer}.
#' @param col1 A \code{character} string for color name.
#' @param col2 A \code{character} string for color name.
#' @param col3 A \code{character} string for color name.
#' @param col4 A \code{character} string for color name.
#' @param col5 A \code{character} string for color name.
#' @return A \code{character} \code{vector} of colors.
#' @importFrom grDevices rgb
mypanel <- function(n,
                    col1 = "navy",
                    col2 = "blue",
                    col3 = "white",
                    col4 = "orange",
                    col5 = "red3") {
  if (length(col1) == 5) {
    col2 <- col1[2]
    col3 <- col1[3]
    col4 <- col1[4]
    col5 <- col1[5]
    col1 <- col1[1]
  }
  col1 <- col2rgb(col1)
  col2 <- col2rgb(col2)
  col3 <- col2rgb(col3)
  col4 <- col2rgb(col4)
  col5 <- col2rgb(col5)
  step <- floor(n / 4)
  red <-
    c(
      seq(col1[1, 1], col2[1, 1], length = step),
      seq(col2[1, 1], col3[1,
                           1], length = step),
      seq(col3[1, 1], col4[1, 1], length = step),
      seq(col4[1,
               1], col5[1, 1], length = n - 3 * step)
    ) / 255
  green <-
    c(
      seq(col1[3, 1], col2[3, 1], length = step),
      seq(col2[3, 1], col3[3,
                           1], length = step),
      seq(col3[3, 1], col4[3, 1], length = step),
      seq(col4[3,
               1], col5[3, 1], length = n - 3 * step)
    ) / 255
  blue <-
    c(
      seq(col1[2, 1], col2[2, 1], length = step),
      seq(col2[2, 1], col3[2,
                           1], length = step),
      seq(col3[2, 1], col4[2, 1], length = step),
      seq(col4[2,
               1], col5[2, 1], length = n - 3 * step)
    ) / 255
  col0 <- rgb(red, blue, green)
  return(col0)
}

#' Creates a color scale (base function).
#'
#' @importFrom gplots colorpanel
#' @param x A \code{vector of numeric} of the data values.
#' @param col1 Color 1
#' @param col2 Color 2
#' @param col3 Color 3
#' @param col4 Color 4
#' @param col5 Color 5
#' @param minx Minimum value.
#' @param maxx Maximum value.
#'
#' @return Vector of colors
colorscale0 <-
  function(x,
           col1 = "navy",
           col2 = "blue",
           col3 = "white",
           col4 = "orange",
           col5 = "red3",
           minx = min(x, na.rm = TRUE),
           maxx = max(x, na.rm = TRUE)) {
    x <- c(minx, maxx, x)
    if (!is.null(col4) & !is.null(col5))
      color0 <- mypanel(10001, col1, col2, col3, col4, col5)
    if (is.null(col4) | is.null(col5)) {
      color0 <- colorpanel(10001, col1, col2, col3)
    }
    color0 <-
      color0[findInterval(x,
                          seq(minx - 1e-06, maxx + 1e-06, length.out = 10001),
                          all.inside = TRUE)]
    color0 <- color0[-c(1:2)]
    return(color0)
  }