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#'Plot Maps of Most Likely Quantiles
#'
#'@author Veronica Torralba, \email{veronica.torralba@bsc.es}, Nicolau Manubens, \email{nicolau.manubens@bsc.es}
#'@description This function receives as main input (via the parameter \code{probs}) a collection of longitude-latitude maps, each containing the probabilities (from 0 to 1) of the different grid cells of belonging to a category. As many categories as maps provided as inputs are understood to exist. The maps of probabilities must be provided on a common rectangular regular grid, and a vector with the longitudes and a vector with the latitudes of the grid must be provided. The input maps can be provided in two forms, either as a list of multiple two-dimensional arrays (one for each category) or as a three-dimensional array, where one of the dimensions corresponds to the different categories.
#'
#'@param probs a list of bi-dimensional arrays with the named dimensions 'latitude' (or 'lat') and 'longitude' (or 'lon'), with equal size and in the same order, or a single tri-dimensional array with an additional dimension (e.g. 'bin') for the different categories. The arrays must contain probability values between 0 and 1, and the probabilities for all categories of a grid cell should not exceed 1 when added.
#'@param lon a numeric vector with the longitudes of the map grid, in the same order as the values along the corresponding dimension in \code{probs}.
#'@param lat a numeric vector with the latitudes of the map grid, in the same order as the values along the corresponding dimension in \code{probs}.
#'@param cat_dim the name of the dimension along which the different categories are stored in \code{probs}. This only applies if \code{probs} is provided in the form of 3-dimensional array. The default expected name is 'bin'.
#'@param bar_titles vector of character strings with the names to be drawn on top of the color bar for each of the categories. As many titles as categories provided in \code{probs} must be provided.
#'@param col_unknown_cat character string with a colour representation of the colour to be used to paint the cells for which no category can be clearly assigned. Takes the value 'white' by default.
#'@param ... additional parameters to be sent to \code{PlotCombinedMap} and \code{PlotEquiMap}.
#'@seealso \code{PlotCombinedMap} and \code{PlotEquiMap}
#'
#'@import s2dverification
#'@importFrom maps map
#'@examples
#'x <- array(1:(20 * 10), dim = c(lat = 10, lon = 20)) / 200
#'a <- x * 0.6
#'b <- (1 - x) * 0.6
#'c <- 1 - (a + b)
#'lons <- seq(0, 360, length = 20)
#'lats <- seq(-90, 90, length = 10)
#'PlotMostLikelyQuantileMap(list(a, b, c), lons, lats,
#' bar_titles = paste('% of belonging to', c('a', 'b', 'c')),
#' brks = 20, width = 10, height = 8)
#'@export
PlotMostLikelyQuantileMap <- function(probs, lon, lat, cat_dim = 'bin',
bar_titles = NULL,
col_unknown_cat = 'white',
...) {
# Check probs
error <- FALSE
if (is.list(probs)) {
if (length(probs) < 1) {
stop("Parameter 'probs' must be of length >= 1 if provided as a list.")
}
check_fun <- function(x) {
is.numeric(x) && (length(dim(x)) == 2)
}
if (!all(sapply(probs, check_fun))) {
error <- TRUE
}
ref_dims <- dim(probs[[1]])
equal_dims <- all(sapply(probs, function(x) identical(dim(x), ref_dims)))
if (!equal_dims) {
stop("All arrays in parameter 'probs' must have the same dimension ",
"sizes and names when 'probs' is provided as a list of arrays.")
}
num_probs <- length(probs)
probs <- unlist(probs)
dim(probs) <- c(ref_dims, map = num_probs)
cat_dim <- 'map'
}
if (!is.numeric(probs)) {
error <- TRUE
}
if (is.null(dim(probs))) {
error <- TRUE
}
if (length(dim(probs)) != 3) {
error <- TRUE
}
if (error) {
stop("Parameter 'probs' must be either a numeric array with 3 dimensions ",
" or a list of numeric arrays of the same size with the 'lon' and ",
"'lat' dimensions.")
}
dimnames <- names(dim(probs))
# Check cat_dim
if (is.character(cat_dim)) {
if (is.null(dimnames)) {
stop("Specified a dimension name in 'cat_dim' but no dimension names provided ",
"in 'probs'.")
}
cat_dim <- which(dimnames == cat_dim)[1]
if (length(cat_dim) != 1) {
stop("Dimension 'cat_dim' not found in 'probs'.")
}
} else if (!is.numeric(cat_dim)) {
stop("Parameter 'cat_dim' must be either a numeric value or a ",
"dimension name.")
}
if (length(cat_dim) != 1) {
stop("Parameter 'cat_dim' must be of length 1.")
}
cat_dim <- round(cat_dim)
nprobs <- dim(probs)[cat_dim]
# Check bar_titles
if (is.null(bar_titles)) {
if (nprobs == 3) {
bar_titles <- list("Below normal (%)", "Normal (%)", "Above normal (%)")
} else if (nprobs == 5) {
bar_titles <- list("Low (%)", "Below normal (%)",
"Normal (%)", "Above normal (%)", "High (%)")
} else {
bar_titles <- paste0("Cat. ", 1:nprobs, " (%)")
}
}
minimum_value <- ceiling(1 / nprobs * 10 * 1.1) * 10
# By now, the PlotCombinedMap function is included below in this file.
# In the future, PlotCombinedMap will be part of s2dverification and will
# be properly imported.
PlotCombinedMap(probs * 100, lon, lat, map_select_fun = max,
display_range = c(minimum_value, 100),
map_dim = cat_dim,
bar_titles = bar_titles,
col_unknown_map = col_unknown_cat, ...)
}
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PlotCombinedMap <- function(maps, lon, lat,
map_select_fun, display_range,
map_dim = 'map',
brks = NULL, cols = NULL,
col_unknown_map = 'white',
mask = NULL, col_mask = 'grey',
bar_titles = NULL, legend_scale = 1,
fileout = NULL, width = 8, height = 5,
size_units = 'in', res = 100,
...) {
# If there is any filenames to store the graphics, process them
# to select the right device
if (!is.null(fileout)) {
deviceInfo <- .SelectDevice(fileout = fileout, width = width, height = height,
units = size_units, res = res)
saveToFile <- deviceInfo$fun
fileout <- deviceInfo$files
}
# Check probs
error <- FALSE
if (is.list(maps)) {
if (length(maps) < 1) {
stop("Parameter 'maps' must be of length >= 1 if provided as a list.")
}
check_fun <- function(x) {
is.numeric(x) && (length(dim(x)) == 2)
}
if (!all(sapply(maps, check_fun))) {
error <- TRUE
}
ref_dims <- dim(maps[[1]])
equal_dims <- all(sapply(maps, function(x) identical(dim(x), ref_dims)))
if (!equal_dims) {
stop("All arrays in parameter 'maps' must have the same dimension ",
"sizes and names when 'maps' is provided as a list of arrays.")
}
num_maps <- length(maps)
maps <- unlist(maps)
dim(maps) <- c(ref_dims, map = num_maps)
map_dim <- 'map'
}
if (!is.numeric(maps)) {
error <- TRUE
}
if (is.null(dim(maps))) {
error <- TRUE
}
if (length(dim(maps)) != 3) {
error <- TRUE
}
if (error) {
stop("Parameter 'maps' must be either a numeric array with 3 dimensions ",
" or a list of numeric arrays of the same size with the 'lon' and ",
"'lat' dimensions.")
}
dimnames <- names(dim(maps))
# Check map_dim
if (is.character(map_dim)) {
if (is.null(dimnames)) {
stop("Specified a dimension name in 'map_dim' but no dimension names provided ",
"in 'maps'.")
}
map_dim <- which(dimnames == map_dim)
if (length(map_dim) < 1) {
stop("Dimension 'map_dim' not found in 'maps'.")
} else {
map_dim <- map_dim[1]
}
} else if (!is.numeric(map_dim)) {
stop("Parameter 'map_dim' must be either a numeric value or a ",
"dimension name.")
}
if (length(map_dim) != 1) {
stop("Parameter 'map_dim' must be of length 1.")
}
map_dim <- round(map_dim)
# Work out lon_dim and lat_dim
lon_dim <- NULL
if (!is.null(dimnames)) {
lon_dim <- which(dimnames %in% c('lon', 'longitude'))[1]
}
if (length(lon_dim) < 1) {
lon_dim <- (1:3)[-map_dim][1]
}
lon_dim <- round(lon_dim)
lat_dim <- NULL
if (!is.null(dimnames)) {
lat_dim <- which(dimnames %in% c('lat', 'latitude'))[1]
}
if (length(lat_dim) < 1) {
lat_dim <- (1:3)[-map_dim][2]
}
lat_dim <- round(lat_dim)
# Check lon
if (!is.numeric(lon)) {
stop("Parameter 'lon' must be a numeric vector.")
}
if (length(lon) != dim(maps)[lon_dim]) {
stop("Parameter 'lon' does not match the longitude dimension in 'maps'.")
# Check lat
if (!is.numeric(lat)) {
stop("Parameter 'lat' must be a numeric vector.")
}
if (length(lat) != dim(maps)[lat_dim]) {
stop("Parameter 'lat' does not match the longitude dimension in 'maps'.")
# Check map_select_fun
if (is.numeric(map_select_fun)) {
if (length(dim(map_select_fun)) != 2) {
stop("Parameter 'map_select_fun' must be an array with dimensions ",
"'lon' and 'lat' if provided as an array.")
}
if (!identical(dim(map_select_fun), dim(maps)[-map_dim])) {
stop("The dimensions 'lon' and 'lat' in the 'map_select_fun' array must ",
"have the same size, name and order as in the 'maps' parameter.")
}
}
if (!is.function(map_select_fun)) {
stop("The parameter 'map_select_fun' must be a function or a numeric array.")
}
# Check display_range
if (!is.numeric(display_range) || length(display_range) != 2) {
stop("Parameter 'display_range' must be a numeric vector of length 2.")
}
# Check brks
if (is.null(brks) || (is.numeric(brks) && length(brks) == 1)) {
num_brks <- 5
if (is.numeric(brks)) {
num_brks <- brks
}
brks <- seq(from = display_range[1], to = display_range[2], length.out = num_brks)
}
if (!is.numeric(brks)) {
stop("Parameter 'brks' must be a numeric vector.")
}
# Check cols
col_sets <- list(c("#A1D99B", "#74C476", "#41AB5D", "#238B45"),
c("#6BAED6FF", "#4292C6FF", "#2171B5FF", "#08519CFF"),
c("#FFEDA0FF", "#FED976FF", "#FEB24CFF", "#FD8D3CFF"),
c("#FC4E2AFF", "#E31A1CFF", "#BD0026FF", "#800026FF"),
c("#FCC5C0", "#FA9FB5", "#F768A1", "#DD3497"))
if (is.null(cols)) {
if (length(col_sets) >= dim(maps)[map_dim]) {
chosen_sets <- 1:(dim(maps)[map_dim])
chosen_sets <- chosen_sets + floor((length(col_sets) - length(chosen_sets)) / 2)
} else {
chosen_sets <- array(1:length(col_sets), dim(maps)[map_dim])
}
cols <- col_sets[chosen_sets]
} else {
if (!is.list(cols)) {
stop("Parameter 'cols' must be a list of character vectors.")
}
if (!all(sapply(cols, is.character))) {
stop("Parameter 'cols' must be a list of character vectors.")
}
if (length(cols) != dim(maps)[map_dim]) {
stop("Parameter 'cols' must be a list of the same length as the number of ",
"maps in 'maps'.")
}
}
for (i in 1:length(cols)) {
if (length(cols[[i]]) != (length(brks) - 1)) {
cols[[i]] <- colorRampPalette(cols[[i]])(length(brks) - 1)
}
}
# Check bar_titles
if (is.null(bar_titles)) {
if (!is.null(names(cols))) {
bar_titles <- names(cols)
} else {
bar_titles <- paste0("Map ", 1:length(cols))
}
} else {
if (!is.character(bar_titles)) {
stop("Parameter 'bar_titles' must be a character vector.")
}
if (length(bar_titles) != length(cols)) {
stop("Parameter 'bar_titles' must be of the same length as the number of ",
"maps in 'maps'.")
# Check legend_scale
if (!is.numeric(legend_scale)) {
stop("Parameter 'legend_scale' must be numeric.")
}
# Check col_unknown_map
if (!is.character(col_unknown_map)) {
stop("Parameter 'col_unknown_map' must be a character string.")
}
# Check col_mask
if (!is.character(col_mask)) {
stop("Parameter 'col_mask' must be a character string.")
}
# Check mask
if (!is.null(mask)) {
if (!is.numeric(mask)) {
stop("Parameter 'mask' must be numeric.")
}
if (length(dim(mask)) != 2) {
stop("Parameter 'mask' must have two dimensions.")
}
if ((dim(mask)[1] != dim(maps)[lat_dim]) ||
(dim(mask)[2] != dim(maps)[lon_dim])) {
stop("Parameter 'mask' must have dimensions c(lat, lon).")
}
#----------------------
# Identify the most likely map
#----------------------
if (is.function(map_select_fun)) {
range_width <- display_range[2] - display_range[1]
ml_map <- apply(maps, c(lat_dim, lon_dim), function(x) {
if (any(is.na(x))) {
res <- NA
} else {
res <- which(x == map_select_fun(x))
if (length(res) > 0) {
res <- res[1]
if (map_select_fun(x) < display_range[1] || map_select_fun(x) > display_range[2]) {
res <- -0.5
} else {
res <- res + (map_select_fun(x) - display_range[1]) / range_width
}
} else {
res <- -0.5
}
}
res
})
} else {
stop("Providing 'map_select_fun' as array not implemented yet.")
ml_map <- map_select_fun
nmap <- dim(maps)[map_dim]
nlat <- length(lat)
nlon <- length(lon)
#----------------------
# Set latitudes from minimum to maximum
#----------------------
if (lat[1] > lat[nlat]){
lat <- lat[nlat:1]
indices <- list(nlat:1, TRUE)
ml_map <- do.call("[", c(list(x = ml_map), indices))
if (!is.null(mask)){
mask <- mask[nlat:1, ]
}
}
#----------------------
# Set layout and parameters
#----------------------
# Open connection to graphical device
if (!is.null(fileout)) {
saveToFile(fileout)
} else if (names(dev.cur()) == 'null device') {
dev.new(units = size_units, res = res, width = width, height = height)
}
plot.new()
par(font.main = 1)
layout(matrix(c(rep(1, nmap),2:(nmap + 1)), 2, nmap, byrow = TRUE), heights = c(6, 1.5))
#----------------------
# Set colors and breaks and then PlotEquiMap
#----------------------
tcols <- c(col_unknown_map, cols[[1]])
for (k in 2:nmap) {
tcols <- append(tcols, c(col_unknown_map, cols[[k]]))
brks_norm <- seq(0, 1, length.out = length(brks))
tbrks <- c(-1, brks_norm + rep(1:nmap, each = length(brks)))
PlotEquiMap(var = ml_map, lon = lon, lat = lat,
brks = tbrks, cols = tcols, drawleg = FALSE,
filled.continents = FALSE, ...)
#----------------------
# Add overplot on top
#----------------------
if (!is.null(mask)) {
cols_mask <- sapply(seq(from = 0, to = 1, length.out = 10),
function(x) adjustcolor(col_mask, alpha.f = x))
image(lon, lat, t(mask), axes = FALSE, col = cols_mask,
breaks = seq(from = 0, to = 1, by = 0.1),
xlab='', ylab='', add = TRUE)
if (!exists('coast_color')) {
coast_color <- 'black'
}
if (min(lon) < 0) {
map('world', interior = FALSE, add = TRUE, lwd = 1, col = coast_color) # Low resolution world map (lon -180 to 180).
} else {
map('world2', interior = FALSE, add = TRUE, lwd = 1, col = coast_color) # Low resolution world map (lon 0 to 360).
}
}
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#----------------------
# Add colorbars
#----------------------
for (k in 1:nmap){
ColorBar(brks = brks, cols = cols[[k]], vertical = FALSE,
draw_separators = TRUE, extra_margin = c(2, 0, 2, 0),
label_scale = legend_scale * 1.5)
if (!is.null(bar_titles)) {
mtext(bar_titles[[k]], 3, line = -3, cex = 1.5)
}
}
# If the graphic was saved to file, close the connection with the device
if (!is.null(fileout)) dev.off()
}
# Once PlotCombined is included in s2dverification and removed from
# CSTools, this function will be removed from CSTools too.
.SelectDevice <- function(fileout, width, height, units, res) {
# This function is used in the plot functions to check the extension of the
# files where the graphics will be stored and select the right R device to
# save them.
# If the vector of filenames ('fileout') has files with different
# extensions, then it will only accept the first one, changing all the rest
# of the filenames to use that extension.
# We extract the extension of the filenames: '.png', '.pdf', ...
ext <- regmatches(fileout, regexpr("\\.[a-zA-Z0-9]*$", fileout))
if (length(ext) != 0) {
# If there is an extension specified, select the correct device
## units of width and height set to accept inches
if (ext[1] == ".png") {
saveToFile <- function(fileout) {
png(filename = fileout, width = width, height = height, res = res, units = units)
}
} else if (ext[1] == ".jpeg") {
saveToFile <- function(fileout) {
jpeg(filename = fileout, width = width, height = height, res = res, units = units)
}
} else if (ext[1] %in% c(".eps", ".ps")) {
saveToFile <- function(fileout) {
postscript(file = fileout, width = width, height = height)
}
} else if (ext[1] == ".pdf") {
saveToFile <- function(fileout) {
pdf(file = fileout, width = width, height = height)
}
} else if (ext[1] == ".svg") {
saveToFile <- function(fileout) {
svg(filename = fileout, width = width, height = height)
}
} else if (ext[1] == ".bmp") {
saveToFile <- function(fileout) {
bmp(filename = fileout, width = width, height = height, res = res, units = units)
}
} else if (ext[1] == ".tiff") {
saveToFile <- function(fileout) {
tiff(filename = fileout, width = width, height = height, res = res, units = units)
}
} else {
warning("file extension not supported, it will be used '.eps' by default.")
## In case there is only one filename
fileout[1] <- sub("\\.[a-zA-Z0-9]*$", ".eps", fileout[1])
ext[1] <- ".eps"
saveToFile <- function(fileout) {
postscript(file = fileout, width = width, height = height)
}
}
# Change filenames when necessary
if (any(ext != ext[1])) {
warning(paste0("some extensions of the filenames provided in 'fileout' are not ", ext[1],". The extensions are being converted to ", ext[1], "."))
fileout <- sub("\\.[a-zA-Z0-9]*$", ext[1], fileout)
}
} else {
# Default filenames when there is no specification
warning("there are no extensions specified in the filenames, default to '.eps'")
fileout <- paste0(fileout, ".eps")
saveToFile <- postscript
}
# return the correct function with the graphical device, and the correct
# filenames
list(fun = saveToFile, files = fileout)