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#' "ROY_BIG_BL" color palette
#'
#' "ROY_BIG_BL", the default palette from the Connectome Workbench.
#'
#' Yields the landmark color hex codes and values for the "ROY_BIG_BL" palette.
#' This is the same color palette as the default Connectome Workbench palette.
#' Source: https://github.com/Washington-University/workbench/blob/master/src/Files/PaletteFile.cxx
#'
#' @param min The minimum value for the color mapping. As in the original
#' palette, the last color (aqua) is actually placed at the bottom .5\% between
#' the minimum and maximum. Default: \code{0}
#' @param max The maximum value for the color mapping. If this value is lower
#' than the minimum, the color mapping will be reversed. If this is equal to
#' the minimum, a palette with only the color black will be returned.
#' Default: \code{1}.
#' @param mid (Optional) The midpoint value for the color mapping. If
#' \code{NULL} (default), the true midpoint is used.
#' @param half \code{"positive"} or \code{"negative"} to use the positive half
#' (black --> red --> yellow) or negative half (black --> blue --> purple -->
#' green --> aqua) only. \code{NULL} (default) or \code{FALSE} to use entire
#' palette.
#' @param pos_half Deprecated. Use \code{half}.
#'
#' @return A data.frame with two columns: \code{"color"} (character: color hex
#' codes) and \code{"value"} (numeric)
#'
#' @importFrom grDevices col2rgb
#'
#' @family coloring
#' @export
#'
ROY_BIG_BL <- function(min=0, max=1, mid=NULL, half=NULL, pos_half=FALSE) {
stopifnot(length(min)==1)
stopifnot(length(max)==1)
if (min==max) {
return( data.frame(color = c("#000000"), value = c(min)) )
}
rev_order <- min > max
if (rev_order) {
temp <- min
min <- max
max <- temp
}
if (pos_half) {
# Deprecated.
half <- "positive"
}
if (is.null(half) || identical(half, FALSE)) {
half <- "no"
}
half <- match.arg(half, c("no", "positive", "negative"))
# Use the same landmark color RGB values, and same spacing. Note the spacing
# is not equidistant between landmarks.
# Added #fff400 at 0.975 to account for the repetition of #00ffff .
# #000000 should be in middle, and the number of colors should be odd.
# The RGB value is 20% toward #ffc800, and .975 is 20% toward .875, so there
# is no visual difference.
color <- c(
"#ffff00", "#fff400", "#ffc800",
"#ff7800", "#ff0000", "#c80000",
"#960000", "#640000", "#3c0000",
"#000000",
"#000050", "#0000aa", "#4b007d",
"#7d00a0", "#4b7d00", "#00c800",
"#00ff00", "#00ffff", "#00ffff"
)
value <- c(
1.000, 0.975, 0.875,
0.750, 0.625, 0.500,
0.375, 0.250, 0.125,
0.000,
-0.125, -0.250, -0.375,
-0.500, -0.625, -0.750,
-0.875, -0.990, -1.000
)
if (half=="positive") {
# Only use the latter half.
value <- value[1:10]
color <- color[1:10]
# Normalize the values to [min, max].
value <- value * (max - min) + min
} else if (half=="negative") {
# Only use the latter half.
value <- value[10:19]
color <- color[10:19]
# Normalize the values to [min, max].
value <- (value + 1) * (max - min) + min
} else {
# Normalize the values to [min, max].
# Note that the bottom 0.5% are all #00ffff.
value <- (value + 1)/2
value <- value * (max - min) + min
# Normalize middle value (black) to mid, if specified.
if (!is.null(mid)) {
if(!(mid > min & mid < max)) { stop("`mid` not between `min` and `max`.") }
old_mid <- (min + max)/2
value[1:9] <- (value[1:9] - old_mid) / (max - old_mid) * (max - mid) + mid
value[10] <- mid
value[11:19] <- (value[11:19] - min) / (old_mid - min) * (mid - min) + min
}
}
if (rev_order) { value <- value[seq(length(value), 1)] }
RBB <- data.frame(color=color, value=value)
RBB[order(value),]
}
#' Make a color palette.
#'
#' Control the mapping of values to colors with \code{colors},
#' \code{color_mode}, and \code{zlim}.
#'
#' There are three kinds of arguments for \code{colors}: \code{"ROY_BIG_BL"},
#' the name of a ColorBrewer palette (see \code{RColorBrewer::brewer.pal.info}
#' and colorbrewer2.org), the name of a viridisLite palette, or a character
#' vector of color names.
#'
#' If \code{colors=="ROY_BIG_BL"}, the "ROY_BIG_BL" palette will be used. It is
#' the same palette as the default for the Connectome Workbench application
#' (https://github.com/Washington-University/workbench/blob/master/src/Files/PaletteFile.cxx).
#' The midpoint will be colored
#' black. From the midpoint toward the upper bound, colors will proceed from
#' black to red to yellow. From the midpoint toward the lower bound, colors
#' will proceed from black to blue to purple to green to aqua. Here is how each
#' color mode behaves if \code{colors=="ROY_BIG_BL"}:
#'
#' \describe{
#' \item{\code{color_mode=="sequential"}}{Only half of the palette will be
#' used. If \code{zlim} is length 2, the higher value will be the maximum and
#' the lower value will be the minimum. Set \code{zlim[1] > zlim[2]} to
#' reverse the color scale. (Note that the second half, black --> red -->
#' yellow, is used by default. To use the negative half specify
#' \code{colors=="ROY_BIG_BL_neg"} instead. It will also be used automatically
#' by \code{xifti_read_surface} when the data range is negative.)
#' \code{zlim} can also be length 10, in which case each value corresponds to
#' the position of an individual color in the half palette.
#' }
#' \item{\code{color_mode=="qualitative"}}{"ROY_BIG_BL" is not recommended for
#' qualitative data, so a warning will be issued. Palette colors will be
#' selected from the landmark "ROY_BIG_BL" colors, with interpolated colors
#' added if the number of colors in the palette (18) is less than this range.
#' \code{zlim} should be a single number: the number of unique colors to get.
#' }
#' \item{\code{color_mode=="diverging"}}{If \code{zlim} is length 2 or 3, the
#' lowest number will be the lower bound and the highest number will
#' be the upper bound. If \code{zlim} is length 3, the middle number will be the
#' midpoint (black). The lower and upper bounds will be aqua and yellow,
#' respectively, except if \code{zlim} is in descending order, in which case
#' the color scale will be reversed (lowest is yellow; highest is aqua).
#' \code{zlim} can also be length 19, in which case each value corresponds to
#' the position of an individual color in the palette.
#' }
#' }
#'
#' If \code{colors} is the name of an RColorBrewer palette (see
#' \code{RColorBrewer::brewer.pal.info}) or viridisLite palette, the colors in
#' that palette will be used, and the following behavior applies.
#' If \code{colors} is a character vector of color names (hex codes or standard
#' R color names), the following behavior applies directly:
#'
#' \describe{
#' \item{\code{color_mode=="sequential"}}{If \code{zlim} is length 2, the
#' higher value will be the maximum and the lower value will be the minimum.
#' Set \code{zlim[1] > zlim[2]} to reverse the color scale. \code{zlim} can
#' also be the same length as the palette, in which case each value
#' corresponds to the position of an individual color in the palette.
#' }
#' \item{\code{color_mode=="qualitative"}}{\code{zlim} should be a single
#' number: the number of unique colors to get. Color interpolation will be
#' used if the number of colors in the palette is less than this range. If
#' \code{length(zlim)==length(colors)}, each color will be mapped to each
#' corresponding value.
#' }
#' \item{\code{color_mode=="diverging"}}{If \code{zlim} is length 2 or 3, the
#' lowest number will be the lower bound and the highest number will
#' be the upper bound. If \code{zlim} is length 3, the middle number will be the
#' midpoint. Set \code{zlim} in descending order to reverse the color scale.
#' \code{zlim} can also be the same length as the palette, in which case each
#' value corresponds to the position of an individual color in the palette.
#' }
#' }
#'
#' @param colors (Optional) "ROY_BIG_BL", the name of a ColorBrewer palette
#' (see \code{RColorBrewer::brewer.pal.info} and colorbrewer2.org), the name of
#' a viridisLite palette, or a character vector of colors.
#' \code{NULL} (default) will use \code{"ROY_BIG_BL"}
#' if \code{color_mode} is \code{"sequential"} or \code{"diverging"}, and
#' \code{"Set2"} if \code{color_mode} is \code{"qualitative"}. See the
#' description for more details.
#' @param color_mode (Optional) \code{"sequential"}, \code{"qualitative"}, or
#' \code{"diverging"}. Default: \code{"sequential"}. See the description for
#' more details.
#' @param zlim (Optional) Controls the mapping of values to each color in
#' \code{colors}. See the description for more details.
#'
#' @return A data.frame with two columns: \code{"color"} (character: color hex
#' codes) and \code{"value"} (numeric)
#'
#' @importFrom RColorBrewer brewer.pal.info brewer.pal
#' @import viridisLite
#'
#' @family coloring
#' @export
#'
make_color_pal <- function(
colors=NULL, color_mode=c("sequential", "qualitative", "diverging"), zlim=NULL) {
# ----------------------------------------------------------------------------
# Check arguments. -----------------------------------------------------------
# ----------------------------------------------------------------------------
color_mode <- match.arg(color_mode, c("sequential", "qualitative", "diverging"))
if (is.null(zlim)) {
zlim <- switch(color_mode,
sequential = c(0, 1),
qualitative = 10,
diverging = c(0, 1)
)
}
# Use default palettes if the colors are not specified.
if (is.null(colors)) {
colors <- switch(
color_mode,
sequential="ROY_BIG_BL", # will use pos half
qualitative="Set2",
diverging="ROY_BIG_BL"
)
}
if (color_mode == "qualitative") {
if (length(zlim) != 1) {
warning("The number of colors will be the first element in `zlim`.\n")
zlim <- zlim[1]
}
stopifnot(zlim > 0)
}
N_COLORS_PRE <- length(colors)
zlim_length <- length(zlim)
# ----------------------------------------------------------------------------
# ROY_BIG_BL -----------------------------------------------------------------
# ----------------------------------------------------------------------------
if ((N_COLORS_PRE == 1) && grepl("ROY_BIG_BL", colors)) {
half <- switch(colors,
ROY_BIG_BL=ifelse(color_mode=="sequential", "pos", "no"),
ROY_BIG_BL_pos="pos",
ROY_BIG_BL_neg="neg"
)
if (color_mode=="sequential") {
if (zlim_length==2) {
pal <- ROY_BIG_BL(zlim[1], zlim[2], half=half)
} else if (zlim_length==10) {
pal <- ROY_BIG_BL(min(zlim), max(zlim), half=half)
pal$value <- zlim
} else {
stop(paste(
"The sequential ROY_BIG_BL palette (default) requires",
"`zlim` to be length 2 (min and max) or 10 (each color)."
))
}
} else if (color_mode=="qualitative") {
ciftiTools_warn(
"The ROY_BIG_BL palette is not recommended for qualitative data."
)
pal <- ROY_BIG_BL(half="no")
pal <- pal[seq(2, nrow(pal)),] # skip duplicate cyan
pal <- expand_color_pal(pal, zlim)[seq(zlim),]
pal$value <- seq(nrow(pal))
} else if (color_mode=="diverging") {
if (zlim_length==2) {
pal <- ROY_BIG_BL(zlim[1], zlim[2], mid=(zlim[1]+zlim[2])/2)
} else if (zlim_length==3) {
pal <- ROY_BIG_BL(zlim[1], zlim[3], mid=zlim[2])
} else if (zlim_length==19) {
pal <- ROY_BIG_BL(min(zlim), max(zlim))
pal$value <- zlim
} else {
stop(paste(
"The diverging ROY_BIG_BL palette requires `zlim` to be length 2",
"(min and max), 3 (min, mid, max), or 19 (each color)."
))
}
}
pal <- pal[order(pal$value),]
rownames(pal) <- NULL
return(pal)
}
# ----------------------------------------------------------------------------
# RColorBrewer / Individual colors -------------------------------------------
# ----------------------------------------------------------------------------
# RColor Brewer --> Individual colors
was_viridis <- FALSE
viridis_cols <- c(
"viridis", "magma", "plasma",
"inferno", "cividis", "mako",
"rocket", "turbo"
)
if ((N_COLORS_PRE == 1) && (colors %in% row.names(brewer.pal.info))) {
colors_info <- brewer.pal.info[row.names(brewer.pal.info) == colors,]
brewer_mode <- match.arg(
as.character(colors_info$category),
c("sequential", "qualitative", "diverging")
)
if (brewer_mode != color_mode) {
warning(paste0(
"The RColorBrewer palette type is ", brewer_mode,
" but the color_mode is ", color_mode, ".\n"
))
}
colors <- brewer.pal(as.numeric(colors_info$maxcolors), colors)
# viridis --> Individual colors
} else if ((N_COLORS_PRE == 1) && (colors %in% viridis_cols)) {
was_viridis <- TRUE
vir_opt <- switch(colors,
magma = "A", inferno = "B", plasma = "C", viridis = "D", cividis = "E",
rocket = "F", mako = "G", turbo="H"
)
colors <- viridisLite::viridis.map[viridisLite::viridis.map$opt==vir_opt,seq(3)]
colors <- apply(colors, 1, function(x){rgb(red=x[1], green=x[2], blue=x[3])})
names(colors) <- NULL
}
# Get `values` for sequential.
if (color_mode == "sequential") {
if (zlim_length==2) {
values <- seq(zlim[1], zlim[2], length.out=length(colors))
} else if (zlim_length == length(colors)) {
values <- zlim
} else {
stop(paste(
"This sequential palette requires `zlim` to be length 2 (min and max)",
" or", length(colors), " (each color)."
))
}
# Get palette for qualitative.
} else if (color_mode=="qualitative") {
pal <- data.frame(color=colors, value=seq(length(colors)))
pal <- expand_color_pal(pal, zlim)
if (was_viridis) {
pal <- pal[round(seq(1,nrow(pal),length.out=zlim)),]
} else {
pal <- pal[seq(zlim),]
}
pal$value <- seq(nrow(pal))
return(pal)
# Get `values` for diverging.
} else if (color_mode=="diverging") {
if (zlim_length==length(colors)) {
values <- zlim
} else {
# Get the minimum, middle, and maximum value for the color scale.
if (zlim_length==2) {
min_val <- zlim[1]
mid_val <- mean(zlim)
max_val <- zlim[2]
} else if (zlim_length==3) {
if (!(all(diff(zlim) > 0) || all(diff(zlim) < 0))) {
warning(paste(
"Sorting `zlim` in ascending order.",
"(Middle value was not between first & last.)"
))
zlim <- sort(zlim)
}
min_val <- zlim[1]
mid_val <- zlim[2]
max_val <- zlim[3]
}
# Interpolate between the min/mid/max to get the color values.
if (length(colors) %% 2 != 1) {
# User probably doesn't care, if there are more than 64 colors
# (e.g. for viridis).
if (length(colors) < 64) {
warning(paste(
"There must be an odd number of colors for the diverging color",
"mode, to have a middle color. Removing the last color."
))
}
colors <- colors[seq(length(colors)-1)]
}
low_vals <- seq(min_val, mid_val, length.out=floor(length(colors)/2)+1)
low_vals <- low_vals[1:(length(low_vals)-1)]
high_vals <- seq(mid_val, max_val, length.out=floor(length(colors)/2)+1)
high_vals <- high_vals[2:length(high_vals)]
values <- c(low_vals, mid_val, high_vals)
}
} else { stop() }
# for sequential and diverging
pal <- data.frame(color=colors, value=values)
pal <- pal[order(pal$value),]
rownames(pal) <- NULL
pal
}
#' Interpolates between entries in the input palette to make a larger palette
#' with COLOR_RES entries.
#'
#' @param pal The color palette to expand, as a data.frame with two columns:
#' \code{"color"} (character: color hex codes) and \code{"value"} (numeric,
#' ascending).
#' @param COLOR_RES The number of entries to have in the output palette.
#'
#' @return A data.frame with two columns: \code{"color"} (character: color hex
#' codes) and \code{"value"} (numeric)
#'
#' @importFrom grDevices colorRampPalette
#'
#' @family coloring
#' @export
#'
expand_color_pal <- function(pal, COLOR_RES=255) {
if (nrow(pal) >= COLOR_RES) { return(pal) }
range <- max(pal$value) - min(pal$value)
if (range == 0) {
vals <- rep(pal$value[1], COLOR_RES)
cols <- as.character( rep(pal$color[1], COLOR_RES) )
} else {
colors <- as.character(pal$color)
# Interpolate between palette values to obtain at least COLOR_RES
# colors levels.
color_res <- COLOR_RES * diff(pal$value)/diff(range(pal$value))
color_res <- as.integer(round(pmax(abs(color_res), 2))) * sign(color_res)
diff_to_fix <- sum(color_res) + 1 - COLOR_RES # +1 b/c last added later
if (diff_to_fix < 0) {
color_res[order(color_res)][seq(-diff_to_fix)] <- color_res[order(color_res)][seq(-diff_to_fix)] + 1
} else if (diff_to_fix > 0) {
color_res[rev(order(color_res))][seq(diff_to_fix)] <- color_res[rev(order(color_res))][seq(diff_to_fix)] - 1
}
vals <- vector(length=0, mode="numeric")
cols <- vector(length=0, mode="character")
for(ii in 1:(nrow(pal)-1)) {
next_vals <- seq(pal$value[ii], pal$value[ii+1], length.out=color_res[ii]+1)
next_vals <- next_vals[seq(length(next_vals)-1)]
next_cols <- colorRampPalette(c(colors[ii], colors[ii+1]), space="Lab")(color_res[ii]+1)
next_cols <- next_cols[seq(length(next_cols)-1)]
vals <- c(vals, next_vals)
cols <- c(cols, next_cols)
}
vals <- c(vals, pal$value[nrow(pal)])
cols <- c(cols, colors[nrow(pal)])
}
pal <- data.frame(color=cols, value=vals)
rownames(pal) <- NULL
pal
}
#' Use a color palette
#'
#' Applies a palette to a data vector to yield a vector of colors.
#'
#' @param data_values The values to map to colors
#' @param pal The palette to use to map values to colors
#' @param color_NA The color to use for \code{NA} values. Default: \code{"white"}.
#' @param indices Return the numeric indices of colors in \code{pal$value}
#' rather than the colors themselves. A value of \code{0} will be used for
#' missing data. Default: \code{FALSE}.
#'
#' @return A character vector of color names (or integers if \code{indices}).
#'
#' @family coloring
#' @export
#'
use_color_pal <- function(data_values, pal, color_NA="white", indices=FALSE) {
stopifnot(is.character(color_NA) && length(color_NA==1))
mask <- is.na(data_values)
# Indices of colors for each datapoint in `data_values`
if (nrow(pal) == 1) {
out <- 1 - as.numeric(mask)
} else {
pal$cut <- -Inf
pal$cut[2:nrow(pal)] <- diff(pal$value)/2 + pal$value[1:(length(pal$value)-1)]
out <- rep(0, length(data_values))
out[!mask] <- as.numeric(cut(as.numeric(data_values[!mask]), c(pal$cut, Inf), right=FALSE))
}
if (!indices) {
out <- c(color_NA, as.character(pal$color))[out + 1]
}
out
}
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