Nothing
R/PlotLayout.R
In s2dverification: Set of Common Tools for Forecast Verification
Defines functions
PlotLayout
Documented in
PlotLayout
#'Arrange and Fill Multi-Pannel Layouts With Optional Colour Bar
#'
#'This function takes an array or list of arrays and loops over each of them
#'to plot all the sub-arrays they contain on an automatically generated
#'multi-pannel layout. A different plot function (not necessarily from
#'s2dverification) can be applied over each of the provided arrays. The input
#'dimensions of each of the functions have to be specified, either with the
#'names or the indices of the corresponding input dimensions. It is possible
#'to draw a common colour bar at any of the sides of the multi-pannel for all
#'the s2dverification plots that use a colour bar. Common plotting arguments
#'for all the arrays in 'var' can be specified via the '...' parameter, and
#'specific plotting arguments for each array can be fully adjusted via
#''special_args'. It is possible to draw titles for each of the figures,
#'layout rows, layout columns and for the whole figure. A number of parameters
#'is provided in order to adjust the position, size and colour of the
#'components. Blank cells can be forced to appear and later be filled in
#'manually with customized plots.\cr
#'This function pops up a blank new device and fills it in, so it cannot be
#'nested in complex layouts.
#'
#'@param fun Plot function (or name of the function) to be called on the
#' arrays provided in 'var'. If multiple arrays are provided in 'var', a
#' vector of as many function names (character strings!) can be provided in
#' 'fun', one for each array in 'var'.
#'@param plot_dims Numeric or character string vector with identifiers of the
#' input plot dimensions of the plot function specified in 'fun'. If
#' character labels are provided, names(dim(var)) or attr('dimensions', var)
#' will be checked to locate the dimensions. As many plots as
#' prod(dim(var)[-plot_dims]) will be generated. If multiple arrays are
#' provided in 'var', 'plot_dims' can be sent a list with a vector of plot
#' dimensions for each. If a single vector is provided, it will be used for
#' all the arrays in 'var'.
#'@param var Multi-dimensional array with at least the dimensions expected by
#' the specified plot function in 'fun'. The dimensions reqired by the
#' function must be specified in 'plot_dims'. The dimensions can be
#' disordered and will be reordered automatically. Dimensions can optionally
#' be labelled in order to refer to them with names in 'plot_dims'. All the
#' available plottable sub-arrays will be automatically plotted and arranged
#' in consecutive cells of an automatically arranged layout. A list of
#' multiple (super-)arrays can be specified. The process will be repeated for
#' each of them, by default applying the same plot function to all of them
#' or, if properly specified in 'fun', a different plot function will be
#' applied to each of them. NAs can be passed to the list: a NA will yield a
#' blank cell in the layout, which can be populated after
#' (see .SwitchToFigure).
#'@param \dots Parameters to be sent to the plotting function 'fun'. If
#' multiple arrays are provided in 'var' and multiple functions are provided
#' in 'fun', the parameters provided through \dots will be sent to all the
#' plot functions, as common parameters. To specify concrete arguments for
#' each of the plot functions see parameter 'special_args'.
#'@param special_args List of sub-lists, each sub-list having specific extra
#' arguments for each of the plot functions provided in 'fun'. If you want to
#' fix a different value for each plot in the layout you can do so by
#' a) splitting your array into a list of sub-arrays (each with the data for
#' one plot) and providing it as parameter 'var',
#' b) providing a list of named sub-lists in 'special_args', where the names
#' of each sub-list match the names of the parameters to be adjusted, and
#' each value in a sub-list contains the value of the corresponding parameter.
#'@param nrow Numeric value to force the number of rows in the automatically
#' generated layout. If higher than the required, this will yield blank cells
#' in the layout (which can then be populated). If lower than the required
#' the function will stop. By default it is configured to arrange the layout
#' in a shape as square as possible. Blank cells can be manually populated
#' after with customized plots (see SwitchTofigure).
#'@param ncol Numeric value to force the number of columns in the
#' automatically generated layout. If higher than the required, this will
#' yield blank cells in the layout (which can then be populated). If lower
#' than the required the function will stop. By default it is configured to
#' arrange the layout in a shape as square as possible. Blank cells can be
#' manually populated after with customized plots (see SwitchTofigure).
#'@param toptitle Topt title for the multi-pannel. Blank by default.
#'@param row_titles Character string vector with titles for each of the rows
#' in the layout. Blank by default.
#'@param col_titles Character string vector with titles for each of the
#' columns in the layout. Blank by default.
#'@param bar_scale Scale factor for the common colour bar. Takes 1 by default.
#'@param title_scale Scale factor for the multi-pannel title. Takes 1 by
#' default.
#'@param title_margin_scale Scale factor for the margins surrounding the top
#' title. Takes 1 by default.
#'@param title_left_shift_scale When plotting row titles, a shift is added
#' to the horizontal positioning of the top title in order to center it to
#' the region of the figures (without taking row titles into account). This
#' shift can be reduced. A value of 0 will remove the shift completely,
#' centering the title to the total width of the device. This parameter will
#' be disregarded if no 'row_titles' are provided.
#'@param subtitle_scale Scale factor for the row titles and column titles
#' (specified in 'row_titles' and 'col_titles'). Takes 1 by default.
#'@param subtitle_margin_scale Scale factor for the margins surrounding the
#' subtitles. Takes 1 by default.
#'@param units Title at the top of the colour bar, most commonly the units of
#' the variable provided in parameter 'var'.
#'@param brks,cols,bar_limits,triangle_ends Usually only providing 'brks' is
#' enough to generate the desired colour bar. These parameters allow to
#' define n breaks that define n - 1 intervals to classify each of the values
#' in 'var'. The corresponding grid cell of a given value in 'var' will be
#' coloured in function of the interval it belongs to. These parameters are
#' sent to \code{ColorBar()} to generate the breaks and colours. Additional
#' colours for values beyond the limits of the colour bar are also generated
#' and applied to the plot if 'bar_limits' or 'brks' and 'triangle_ends' are
#' properly provided to do so. See ?ColorBar for a full explanation.
#'@param col_inf,col_sup Colour identifiers to colour the values in 'var' that
#' go beyond the extremes of the colour bar and to colour NA values,
#' respectively. 'colNA' takes 'white' by default. 'col_inf' and 'col_sup'
#' will take the value of 'colNA' if not specified. See ?ColorBar for a full
#' explanation on 'col_inf' and 'col_sup'.
#'@param color_fun,subsampleg,bar_extra_labels,draw_bar_ticks,draw_separators,triangle_ends_scale,bar_label_digits,bar_label_scale,units_scale,bar_tick_scale,bar_extra_margin Set of parameters to control the visual aspect of the drawn colour bar. See ?ColorBar for a full explanation.
#'@param drawleg Where to draw the common colour bar. Can take values TRUE,
#' FALSE or:\cr
#' 'up', 'u', 'U', 'top', 't', 'T', 'north', 'n', 'N'\cr
#' 'down', 'd', 'D', 'bottom', 'b', 'B', 'south', 's', 'S' (default)\cr
#' 'right', 'r', 'R', 'east', 'e', 'E'\cr
#' 'left', 'l', 'L', 'west', 'w', 'W'
#'@param titles Character string vector with titles for each of the figures in
#' the multi-pannel, from top-left to bottom-right. Blank by default.
#'@param bar_left_shift_scale When plotting row titles, a shift is added to
#' the horizontal positioning of the colour bar in order to center it to the
#' region of the figures (without taking row titles into account). This shift
#' can be reduced. A value of 0 will remove the shift completely, centering
#' the colour bar to the total width of the device. This parameter will be
#' disregarded if no 'row_titles' are provided.
#'@param extra_margin Extra margins to be added around the layout, in the
#' format c(y1, x1, y2, x2). The units are margin lines. Takes rep(0, 4)
#' by default.
#'@param fileout File where to save the plot. If not specified (default) a
#' graphics device will pop up. Extensions allowed: eps/ps, jpeg, png, pdf,
#' bmp and tiff.
#'@param width Width in inches of the multi-pannel. 7 by default, or 11 if
#' 'fielout' has been specified.
#'@param height Height in inches of the multi-pannel. 7 by default, or 11 if
#' 'fileout' has been specified.
#'@param size_units Units of the size of the device (file or window) to plot
#' in. Inches ('in') by default. See ?Devices and the creator function of
#' the corresponding device.
#'@param res Resolution of the device (file or window) to plot in. See
#' ?Devices and the creator function of the corresponding device.
#'@param close_device Whether to close the graphics device after plotting
#' the layout and a 'fileout' has been specified. This is useful to avoid
#' closing the device when saving the layout into a file and willing to add
#' extra elements or figures. Takes TRUE by default. Disregarded if no
#' 'fileout' has been specified.
#'
#'@return
#'\item{brks}{
#' Breaks used for colouring the map (and legend if drawleg = TRUE).
#'}
#'\item{cols}{
#' Colours used for colouring the map (and legend if drawleg = TRUE).
#' Always of length length(brks) - 1.
#'}
#'\item{col_inf}{
#' Colour used to draw the lower triangle end in the colour bar
#' (NULL if not drawn at all).
#'}
#'\item{col_sup}{
#' Colour used to draw the upper triangle end in the colour bar
#' (NULL if not drawn at all).
#'}
#'\item{layout_matrix}{
#' Underlying matrix of the layout. Useful to later set any of the layout
#' cells as current figure to add plot elements. See .SwitchToFigure.
#'}
#'
#'@keywords dynamic
#'@author History:\cr
#' 0.1 - 2016-08 (N. Manubens) - Original code
#'@examples
#'# See examples on Load() to understand the first lines in this example
#' \dontrun{
#'data_path <- system.file('sample_data', package = 's2dverification')
#'expA <- list(name = 'experiment', path = file.path(data_path,
#' 'model/$EXP_NAME$/$STORE_FREQ$_mean/$VAR_NAME$_3hourly',
#' '$VAR_NAME$_$START_DATE$.nc'))
#'obsX <- list(name = 'observation', path = file.path(data_path,
#' '$OBS_NAME$/$STORE_FREQ$_mean/$VAR_NAME$',
#' '$VAR_NAME$_$YEAR$$MONTH$.nc'))
#'
#'# Now we are ready to use Load().
#'startDates <- c('19851101', '19901101', '19951101', '20001101', '20051101')
#'sampleData <- Load('tos', list(expA), list(obsX), startDates,
#' leadtimemin = 1, leadtimemax = 4, output = 'lonlat',
#' latmin = 27, latmax = 48, lonmin = -12, lonmax = 40)
#' }
#' \dontshow{
#'startDates <- c('19851101', '19901101', '19951101', '20001101', '20051101')
#'sampleData <- s2dverification:::.LoadSampleData('tos', c('experiment'),
#' c('observation'), startDates,
#' leadtimemin = 1,
#' leadtimemax = 4,
#' output = 'lonlat',
#' latmin = 27, latmax = 48,
#' lonmin = -12, lonmax = 40)
#' }
#'PlotLayout(PlotEquiMap, c('lat', 'lon'), sampleData$mod[1, , 1, 1, , ],
#' sampleData$lon, sampleData$lat,
#' toptitle = 'Predicted tos for Nov 1960 from 1st Nov',
#' titles = paste('Member', 1:15))
#'
#'@importFrom grDevices dev.cur dev.new dev.off
#'@export
PlotLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
nrow = NULL, ncol = NULL, toptitle = NULL,
row_titles = NULL, col_titles = NULL, bar_scale = 1,
title_scale = 1, title_margin_scale = 1,
title_left_shift_scale = 1,
subtitle_scale = 1, subtitle_margin_scale = 1,
brks = NULL, cols = NULL, drawleg = 'S', titles = NULL,
subsampleg = NULL, bar_limits = NULL,
triangle_ends = NULL, col_inf = NULL, col_sup = NULL,
color_fun = clim.colors,
draw_bar_ticks = TRUE, draw_separators = FALSE,
triangle_ends_scale = 1, bar_extra_labels = NULL,
units = NULL, units_scale = 1, bar_label_scale = 1,
bar_tick_scale = 1, bar_extra_margin = rep(0, 4),
bar_left_shift_scale = 1, bar_label_digits = 4,
extra_margin = rep(0, 4),
fileout = NULL, width = NULL, height = NULL,
size_units = 'in', res = 100, close_device = TRUE) {
# 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
}
is_single_na <- function(x) ifelse(length(x) > 1, FALSE, is.na(x))
# Check var
if (is.array(var) || (is_single_na(var))) {
var <- list(var)
} else if (is.list(var)) {
if (!all(sapply(var, is.array) | sapply(var, is_single_na))) {
stop("Parameter 'var' must be an array or a list of arrays (or NA values).")
}
} else {
stop("Parameter 'var' must be an array or a list of arrays.")
}
# Check fun
if (length(fun) == 1) {
if (is.function(fun)) {
fun <- as.character(substitute(fun))
}
if (is.character(fun)) {
fun <- rep(fun, length(var))
}
}
if (!is.character(fun) || (length(fun) != length(var))) {
stop("Parameter 'fun' must be a single function or a vector of function names, one for each array provided in parameter 'var'.")
}
# Check special_args
if (!is.null(special_args)) {
if (!is.list(special_args) || any(!sapply(special_args, is.list))) {
stop("Parameter 'special_args' must be a list of lists.")
} else if (length(special_args) != length(var)) {
stop("Parameter 'special_args' must contain a list of special arguments for each array provided in 'var'.")
}
}
# Check plot_dims
if (is.character(plot_dims) || is.numeric(plot_dims)) {
plot_dims <- replicate(length(var), plot_dims, simplify = FALSE)
}
if (!is.list(plot_dims) || !all(sapply(plot_dims, is.character) | sapply(plot_dims, is.numeric)) ||
(length(plot_dims) != length(var))) {
stop("Parameter 'plot_dims' must contain a single numeric or character vector with dimension identifiers or a vector for each array provided in parameter 'var'.")
}
# Check nrow
if (!is.null(nrow)) {
if (!is.numeric(nrow)) {
stop("Parameter 'nrow' must be numeric or NULL.")
}
nrow <- round(nrow)
}
# Check ncol
if (!is.null(ncol)) {
if (!is.numeric(ncol)) {
stop("Parameter 'ncol' must be numeric or NULL.")
}
ncol <- round(ncol)
}
# Check toptitle
if (is.null(toptitle) || is.na(toptitle)) {
toptitle <- ''
}
if (!is.character(toptitle)) {
stop("Parameter 'toptitle' must be a character string.")
}
# Check row_titles
if (!is.null(row_titles)) {
if (!is.character(row_titles)) {
stop("Parameter 'row_titles' must be a vector of character strings.")
}
}
# Check col_titles
if (!is.null(row_titles)) {
if (!is.character(row_titles)) {
stop("Parameter 'row_titles' must be a vector of character strings.")
}
}
# Check drawleg
if (is.character(drawleg)) {
if (drawleg %in% c('up', 'u', 'U', 'top', 't', 'T', 'north', 'n', 'N')) {
drawleg <- 'N'
} else if (drawleg %in% c('down', 'd', 'D', 'bottom', 'b', 'B', 'south', 's', 'S')) {
drawleg <- 'S'
} else if (drawleg %in% c('right', 'r', 'R', 'east', 'e', 'E')) {
drawleg <- 'E'
} else if (drawleg %in% c('left', 'l', 'L', 'west', 'w', 'W')) {
drawleg <- 'W'
} else {
stop("Parameter 'drawleg' must be either TRUE, FALSE or a valid identifier of a position (see ?PlotMultiMap).")
}
} else if (!is.logical(drawleg)) {
stop("Parameter 'drawleg' must be either TRUE, FALSE or a valid identifier of a position (see ?PlotMultiMap).")
}
if (drawleg != FALSE && all(sapply(var, is_single_na)) &&
(is.null(brks) || length(brks) < 2)) {
stop("Either data arrays in 'var' or breaks in 'brks' must be provided if 'drawleg' is requested.")
}
# Check the rest of parameters (unless the user simply wants to build an empty layout)
var_limits <- NULL
if (!all(sapply(var, is_single_na))) {
var_limits <- c(min(unlist(var), na.rm = TRUE), max(unlist(var), na.rm = TRUE))
if ((any(is.infinite(var_limits)) || var_limits[1] == var_limits[2])) {
stop("Arrays in parameter 'var' must contain at least 2 different values.")
}
}
colorbar <- ColorBar(brks, cols, FALSE, subsampleg, bar_limits,
var_limits, triangle_ends, col_inf, col_sup, color_fun,
plot = FALSE, draw_bar_ticks,
draw_separators, triangle_ends_scale, bar_extra_labels,
units, units_scale, bar_label_scale, bar_tick_scale,
bar_extra_margin, bar_label_digits)
# Check bar_scale
if (!is.numeric(bar_scale)) {
stop("Parameter 'bar_scale' must be numeric.")
}
# Check bar_left_shift_scale
if (!is.numeric(bar_left_shift_scale)) {
stop("Parameter 'bar_left_shift_scale' must be numeric.")
}
# Check title_scale
if (!is.numeric(title_scale)) {
stop("Parameter 'title_scale' must be numeric.")
}
# Check title_margin_scale
if (!is.numeric(title_margin_scale)) {
stop("Parameter 'title_margin_scale' must be numeric.")
}
# Check title_left_shift_scale
if (!is.numeric(title_left_shift_scale)) {
stop("Parameter 'title_left_shift_scale' must be numeric.")
}
# Check subtitle_scale
if (!is.numeric(subtitle_scale)) {
stop("Parameter 'subtite_scale' must be numeric.")
}
# Check subtitle_margin_scale
if (!is.numeric(subtitle_margin_scale)) {
stop("Parameter 'subtite_margin_scale' must be numeric.")
}
# Check titles
if (!all(sapply(titles, is.character))) {
stop("Parameter 'titles' must be a vector of character strings.")
}
# Check extra_margin
if (!is.numeric(extra_margin) || length(extra_margin) != 4) {
stop("Parameter 'extra_margin' must be a numeric vector with 4 elements.")
}
# Check width
if (is.null(width)) {
if (is.null(fileout)) {
width <- 7
} else {
width <- 11
}
}
if (!is.numeric(width)) {
stop("Parameter 'width' must be numeric.")
}
# Check height
if (is.null(height)) {
if (is.null(fileout)) {
height <- 7
} else {
height <- 8
}
}
if (!is.numeric(height)) {
stop("Parameter 'height' must be numeric.")
}
# Check close_device
if (!is.logical(close_device)) {
stop("Parameter 'close_device' must be logical.")
}
# Count the total number of maps and reorder each array of maps to have the lat and lon dimensions at the end.
n_plots <- 0
plot_array_i <- 1
for (plot_array in var) {
if (is_single_na(plot_array)) {
n_plots <- n_plots + 1
} else {
dim_ids <- plot_dims[[plot_array_i]]
if (is.character(dim_ids)) {
dimnames <- NULL
if (!is.null(names(dim(plot_array)))) {
dimnames <- names(dim(plot_array))
} else if (!is.null(attr(plot_array, 'dimensions'))) {
dimnames <- attr(plot_array, 'dimensions')
}
if (!is.null(dimnames)) {
if (any(!sapply(dim_ids, `%in%`, dimnames))) {
stop("All arrays provided in parameter 'var' must have all the dimensions in 'plot_dims'.")
}
dim_ids <- sapply(dim_ids, function(x) which(dimnames == x)[1])
var[[plot_array_i]] <- .aperm2(var[[plot_array_i]], c((1:length(dim(plot_array)))[-dim_ids], dim_ids))
} else {
.warning(paste0("Assuming the ", plot_array_i, "th array provided in 'var' has 'plot_dims' as last dimensions (right-most)."))
dims <- tail(c(rep(1, length(dim_ids)), dim(plot_array)), length(dim_ids))
dim_ids <- tail(1:length(dim(plot_array)), length(dim_ids))
if (length(dim(var[[plot_array_i]])) < length(dims)) {
dim(var[[plot_array_i]]) <- dims
}
}
} else if (any(dim_ids > length(dim(plot_array)))) {
stop("Parameter 'plot_dims' contains dimension identifiers out of range.")
}
n_plots <- n_plots + prod(dim(plot_array)[-dim_ids])
#n_plots <- n_plots + prod(head(c(rep(1, length(dim_ids)), dim(plot_array)), length(dim(plot_array))))
if (length(dim(var[[plot_array_i]])) == length(dim_ids)) {
dim(var[[plot_array_i]]) <- c(1, dim(var[[plot_array_i]]))
dim_ids <- dim_ids + 1
}
plot_dims[[plot_array_i]] <- dim_ids
}
plot_array_i <- plot_array_i + 1
}
if (is.null(nrow) && is.null(ncol)) {
ncol <- ceiling(sqrt(n_plots))
nrow <- ceiling(n_plots/ncol)
} else if (is.null(ncol)) {
ncol <- ceiling(n_plots/nrow)
} else if (is.null(nrow)) {
nrow <- ceiling(n_plots/ncol)
} else if (nrow * ncol < n_plots) {
stop("There are more arrays to plot in 'var' than cells defined by 'nrow' x 'ncol'.")
}
if (is.logical(drawleg) && drawleg) {
if (nrow > ncol) {
drawleg <- 'S'
} else {
drawleg <- 'E'
}
}
vertical <- drawleg %in% c('E', 'W')
# 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)
} else if (prod(par('mfrow')) > 1) {
dev.new(units = units, res = res, width = width, height = height)
}
# Take size of device and set up layout:
# ---------------------------------------------
# |0000000000000000000000000000000000000000000|
# |0000000000000000 TOP TITLE 0000000000000000|
# |0000000000000000000000000000000000000000000|
# |-------------------------------------------|
# |00000|0000000000000000000000000000000000000|
# |00000|000000000000 ROW TITLES 0000000000000|
# |00000|0000000000000000000000000000000000000|
# |00000|-------------------------------------|
# |0 0|222222222222222222|333333333333333333|
# |0 C 0|222222222222222222|333333333333333333|
# |0 O 0|222222222222222222|333333333333333333|
# |0 L 0|2222 FIGURE 1 2222|3333 FIGURE 2 3333|
# |0 0|222222222222222222|333333333333333333|
# |0 T 0|222222222222222222|333333333333333333|
# |0 I 0|222222222222222222|333333333333333333|
# |0 T 0|-------------------------------------|
# |0 L 0|444444444444444444|555555555555555555|
# |0 S 0|444444444444444444|555555555555555555|
# |0 0|444444444444444444|555555555555555555|
# |00000|4444 FIGURE 3 4444|5555 FIGURE 4 5555|
# |00000|444444444444444444|555555555555555555|
# |00000|444444444444444444|555555555555555555|
# |00000|444444444444444444|555555555555555555|
# |-------------------------------------------|
# |1111111111111111111111111111111111111111111|
# |1111111111111111 COLOR BAR 1111111111111111|
# |1111111111111111111111111111111111111111111|
# ---------------------------------------------
device_size <- par('din')
device_size[1] <- device_size[1] - sum(extra_margin[c(2, 4)])
device_size[2] <- device_size[2] - sum(extra_margin[c(1, 3)])
cs <- char_size <- par('csi')
title_cex <- 2.5 * title_scale
title_margin <- 0.5 * title_cex * title_margin_scale
subtitle_cex <- 1.5 * subtitle_scale
subtitle_margin <- 0.5 * sqrt(nrow * ncol) * subtitle_cex * subtitle_margin_scale
mat_layout <- 1:(nrow * ncol) + ifelse(drawleg != FALSE, 1, 0)
mat_layout <- matrix(mat_layout, nrow, ncol, byrow = TRUE)
fsu <- figure_size_units <- 10 # unitless
widths <- rep(fsu, ncol)
heights <- rep(fsu, nrow)
n_figures <- nrow * ncol
if (length(row_titles) > 0) {
mat_layout <- cbind(rep(0, dim(mat_layout)[1]), mat_layout)
widths <- c(((subtitle_cex + subtitle_margin / 2) * cs / device_size[1]) * ncol * fsu, widths)
}
if (length(col_titles) > 0) {
mat_layout <- rbind(rep(0, dim(mat_layout)[2]), mat_layout)
heights <- c(((subtitle_cex + subtitle_margin) * cs / device_size[2]) * nrow * fsu, heights)
}
if (drawleg != FALSE) {
if (drawleg == 'N') {
mat_layout <- rbind(rep(1, dim(mat_layout)[2]), mat_layout)
heights <- c(round(bar_scale * 2 * nrow), heights)
} else if (drawleg == 'S') {
mat_layout <- rbind(mat_layout, rep(1, dim(mat_layout)[2]))
heights <- c(heights, round(bar_scale * 2 * nrow))
} else if (drawleg == 'W') {
mat_layout <- cbind(rep(1, dim(mat_layout)[1]), mat_layout)
widths <- c(round(bar_scale * 3 * ncol), widths)
} else if (drawleg == 'E') {
mat_layout <- cbind(mat_layout, rep(1, dim(mat_layout)[1]))
widths <- c(widths, round(bar_scale * 3 * ncol))
}
n_figures <- n_figures + 1
}
if (toptitle != '') {
mat_layout <- rbind(rep(0, dim(mat_layout)[2]), mat_layout)
heights <- c(((title_cex + title_margin) * cs / device_size[2]) * nrow * fsu, heights)
}
par(oma = extra_margin)
layout(mat_layout, widths, heights)
# Draw the color bar
if (drawleg != FALSE) {
if (length(row_titles) > 0) {
bar_extra_margin[2] <- bar_extra_margin[2] + (subtitle_cex + subtitle_margin / 2) *
bar_left_shift_scale
}
ColorBar(colorbar$brks, colorbar$cols, vertical, subsampleg,
bar_limits, var_limits,
triangle_ends = triangle_ends, col_inf = colorbar$col_inf,
col_sup = colorbar$col_sup, color_fun, plot = TRUE, draw_bar_ticks,
draw_separators, triangle_ends_scale, bar_extra_labels,
units, units_scale, bar_label_scale, bar_tick_scale,
bar_extra_margin, bar_label_digits)
}
# Draw titles
if (toptitle != '' || length(col_titles) > 0 || length(row_titles) > 0) {
plot(0, type = 'n', ann = FALSE, axes = FALSE, xaxs = 'i', yaxs = 'i',
xlim = c(0, 1), ylim = c(0, 1))
width_lines <- par('fin')[1] / par('csi')
plot_lines <- par('pin')[1] / par('csi')
plot_range <- par('xaxp')[2] - par('xaxp')[1]
size_units_per_line <- plot_range / plot_lines
if (toptitle != '') {
title_x_center <- par('xaxp')[1] - par('mar')[2] * size_units_per_line +
ncol * width_lines * size_units_per_line / 2
if (length(row_titles) > 0) {
title_x_center <- title_x_center - (1 - title_left_shift_scale) *
(subtitle_cex + subtitle_margin) / 2 * size_units_per_line
}
title_y_center <- par('mar')[3] + (title_margin + title_cex) / 2
if (length(col_titles > 0)) {
title_y_center <- title_y_center + (subtitle_margin + subtitle_cex)
}
mtext(toptitle, cex = title_cex, line = title_y_center, at = title_x_center,
padj = 0.5)
}
if (length(col_titles) > 0) {
t_x_center <- par('xaxp')[1] - par('mar')[2] * size_units_per_line
for (t in 1:ncol) {
mtext(col_titles[t], cex = subtitle_cex,
line = par('mar')[3] + (subtitle_margin + subtitle_cex) / 2,
at = t_x_center + (t - 0.5) * width_lines * size_units_per_line,
padj = 0.5)
}
}
height_lines <- par('fin')[2] / par('csi')
plot_lines <- par('pin')[2] / par('csi')
plot_range <- par('yaxp')[2] - par('yaxp')[1]
size_units_per_line <- plot_range / plot_lines
if (length(row_titles) > 0) {
t_y_center <- par('yaxp')[1] - par('mar')[1] * size_units_per_line
for (t in 1:nrow) {
mtext(row_titles[t], cex = subtitle_cex,
line = par('mar')[2] + (subtitle_margin + subtitle_cex) / 2,
at = t_y_center - (t - 1.5) * height_lines * size_units_per_line,
padj = 0.5, side = 2)
}
}
par(new = TRUE)
}
array_number <- 1
plot_number <- 1
# For each array provided in var
lapply(var, function(x) {
if (is_single_na(x)) {
if (!all(sapply(var[array_number:length(var)], is_single_na))) {
plot.new()
par(new = FALSE)
}
plot_number <<- plot_number + 1
} else {
if (is.character(plot_dims[[array_number]])) {
plot_dim_indices <- which(names(dim(x)) %in% plot_dims[[array_number]])
} else {
plot_dim_indices <- plot_dims[[array_number]]
}
# For each of the arrays provided in that array
apply(x, (1:length(dim(x)))[-plot_dim_indices],
function(y) {
# Do the plot
fun_args <- c(list(y, toptitle = titles[plot_number]), list(...),
special_args[[array_number]])
funct <- fun[[array_number]]
if (fun[[array_number]] %in% c('PlotEquiMap', 'PlotStereoMap', 'PlotSection')) {
fun_args <- c(fun_args, list(brks = colorbar$brks, cols = colorbar$cols,
col_inf = colorbar$col_inf,
col_sup = colorbar$col_sup,
drawleg = FALSE))
}
do.call(fun[[array_number]], fun_args)
plot_number <<- plot_number + 1
})
}
array_number <<- array_number + 1
})
# If the graphic was saved to file, close the connection with the device
if (!is.null(fileout) && close_device) dev.off()
invisible(list(brks = colorbar$brks, cols = colorbar$cols,
col_inf = colorbar$col_inf, col_sup = colorbar$col_sup,
layout_matrix = mat_layout))
}
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Defines functions PlotLayout
Documented in PlotLayout
#'Arrange and Fill Multi-Pannel Layouts With Optional Colour Bar
#'
#'This function takes an array or list of arrays and loops over each of them
#'to plot all the sub-arrays they contain on an automatically generated
#'multi-pannel layout. A different plot function (not necessarily from
#'s2dverification) can be applied over each of the provided arrays. The input
#'dimensions of each of the functions have to be specified, either with the
#'names or the indices of the corresponding input dimensions. It is possible
#'to draw a common colour bar at any of the sides of the multi-pannel for all
#'the s2dverification plots that use a colour bar. Common plotting arguments
#'for all the arrays in 'var' can be specified via the '...' parameter, and
#'specific plotting arguments for each array can be fully adjusted via
#''special_args'. It is possible to draw titles for each of the figures,
#'layout rows, layout columns and for the whole figure. A number of parameters
#'is provided in order to adjust the position, size and colour of the
#'components. Blank cells can be forced to appear and later be filled in
#'manually with customized plots.\cr
#'This function pops up a blank new device and fills it in, so it cannot be
#'nested in complex layouts.
#'
#'@param fun Plot function (or name of the function) to be called on the
#' arrays provided in 'var'. If multiple arrays are provided in 'var', a
#' vector of as many function names (character strings!) can be provided in
#' 'fun', one for each array in 'var'.
#'@param plot_dims Numeric or character string vector with identifiers of the
#' input plot dimensions of the plot function specified in 'fun'. If
#' character labels are provided, names(dim(var)) or attr('dimensions', var)
#' will be checked to locate the dimensions. As many plots as
#' prod(dim(var)[-plot_dims]) will be generated. If multiple arrays are
#' provided in 'var', 'plot_dims' can be sent a list with a vector of plot
#' dimensions for each. If a single vector is provided, it will be used for
#' all the arrays in 'var'.
#'@param var Multi-dimensional array with at least the dimensions expected by
#' the specified plot function in 'fun'. The dimensions reqired by the
#' function must be specified in 'plot_dims'. The dimensions can be
#' disordered and will be reordered automatically. Dimensions can optionally
#' be labelled in order to refer to them with names in 'plot_dims'. All the
#' available plottable sub-arrays will be automatically plotted and arranged
#' in consecutive cells of an automatically arranged layout. A list of
#' multiple (super-)arrays can be specified. The process will be repeated for
#' each of them, by default applying the same plot function to all of them
#' or, if properly specified in 'fun', a different plot function will be
#' applied to each of them. NAs can be passed to the list: a NA will yield a
#' blank cell in the layout, which can be populated after
#' (see .SwitchToFigure).
#'@param \dots Parameters to be sent to the plotting function 'fun'. If
#' multiple arrays are provided in 'var' and multiple functions are provided
#' in 'fun', the parameters provided through \dots will be sent to all the
#' plot functions, as common parameters. To specify concrete arguments for
#' each of the plot functions see parameter 'special_args'.
#'@param special_args List of sub-lists, each sub-list having specific extra
#' arguments for each of the plot functions provided in 'fun'. If you want to
#' fix a different value for each plot in the layout you can do so by
#' a) splitting your array into a list of sub-arrays (each with the data for
#' one plot) and providing it as parameter 'var',
#' b) providing a list of named sub-lists in 'special_args', where the names
#' of each sub-list match the names of the parameters to be adjusted, and
#' each value in a sub-list contains the value of the corresponding parameter.
#'@param nrow Numeric value to force the number of rows in the automatically
#' generated layout. If higher than the required, this will yield blank cells
#' in the layout (which can then be populated). If lower than the required
#' the function will stop. By default it is configured to arrange the layout
#' in a shape as square as possible. Blank cells can be manually populated
#' after with customized plots (see SwitchTofigure).
#'@param ncol Numeric value to force the number of columns in the
#' automatically generated layout. If higher than the required, this will
#' yield blank cells in the layout (which can then be populated). If lower
#' than the required the function will stop. By default it is configured to
#' arrange the layout in a shape as square as possible. Blank cells can be
#' manually populated after with customized plots (see SwitchTofigure).
#'@param toptitle Topt title for the multi-pannel. Blank by default.
#'@param row_titles Character string vector with titles for each of the rows
#' in the layout. Blank by default.
#'@param col_titles Character string vector with titles for each of the
#' columns in the layout. Blank by default.
#'@param bar_scale Scale factor for the common colour bar. Takes 1 by default.
#'@param title_scale Scale factor for the multi-pannel title. Takes 1 by
#' default.
#'@param title_margin_scale Scale factor for the margins surrounding the top
#' title. Takes 1 by default.
#'@param title_left_shift_scale When plotting row titles, a shift is added
#' to the horizontal positioning of the top title in order to center it to
#' the region of the figures (without taking row titles into account). This
#' shift can be reduced. A value of 0 will remove the shift completely,
#' centering the title to the total width of the device. This parameter will
#' be disregarded if no 'row_titles' are provided.
#'@param subtitle_scale Scale factor for the row titles and column titles
#' (specified in 'row_titles' and 'col_titles'). Takes 1 by default.
#'@param subtitle_margin_scale Scale factor for the margins surrounding the
#' subtitles. Takes 1 by default.
#'@param units Title at the top of the colour bar, most commonly the units of
#' the variable provided in parameter 'var'.
#'@param brks,cols,bar_limits,triangle_ends Usually only providing 'brks' is
#' enough to generate the desired colour bar. These parameters allow to
#' define n breaks that define n - 1 intervals to classify each of the values
#' in 'var'. The corresponding grid cell of a given value in 'var' will be
#' coloured in function of the interval it belongs to. These parameters are
#' sent to \code{ColorBar()} to generate the breaks and colours. Additional
#' colours for values beyond the limits of the colour bar are also generated
#' and applied to the plot if 'bar_limits' or 'brks' and 'triangle_ends' are
#' properly provided to do so. See ?ColorBar for a full explanation.
#'@param col_inf,col_sup Colour identifiers to colour the values in 'var' that
#' go beyond the extremes of the colour bar and to colour NA values,
#' respectively. 'colNA' takes 'white' by default. 'col_inf' and 'col_sup'
#' will take the value of 'colNA' if not specified. See ?ColorBar for a full
#' explanation on 'col_inf' and 'col_sup'.
#'@param color_fun,subsampleg,bar_extra_labels,draw_bar_ticks,draw_separators,triangle_ends_scale,bar_label_digits,bar_label_scale,units_scale,bar_tick_scale,bar_extra_margin Set of parameters to control the visual aspect of the drawn colour bar. See ?ColorBar for a full explanation.
#'@param drawleg Where to draw the common colour bar. Can take values TRUE,
#' FALSE or:\cr
#' 'up', 'u', 'U', 'top', 't', 'T', 'north', 'n', 'N'\cr
#' 'down', 'd', 'D', 'bottom', 'b', 'B', 'south', 's', 'S' (default)\cr
#' 'right', 'r', 'R', 'east', 'e', 'E'\cr
#' 'left', 'l', 'L', 'west', 'w', 'W'
#'@param titles Character string vector with titles for each of the figures in
#' the multi-pannel, from top-left to bottom-right. Blank by default.
#'@param bar_left_shift_scale When plotting row titles, a shift is added to
#' the horizontal positioning of the colour bar in order to center it to the
#' region of the figures (without taking row titles into account). This shift
#' can be reduced. A value of 0 will remove the shift completely, centering
#' the colour bar to the total width of the device. This parameter will be
#' disregarded if no 'row_titles' are provided.
#'@param extra_margin Extra margins to be added around the layout, in the
#' format c(y1, x1, y2, x2). The units are margin lines. Takes rep(0, 4)
#' by default.
#'@param fileout File where to save the plot. If not specified (default) a
#' graphics device will pop up. Extensions allowed: eps/ps, jpeg, png, pdf,
#' bmp and tiff.
#'@param width Width in inches of the multi-pannel. 7 by default, or 11 if
#' 'fielout' has been specified.
#'@param height Height in inches of the multi-pannel. 7 by default, or 11 if
#' 'fileout' has been specified.
#'@param size_units Units of the size of the device (file or window) to plot
#' in. Inches ('in') by default. See ?Devices and the creator function of
#' the corresponding device.
#'@param res Resolution of the device (file or window) to plot in. See
#' ?Devices and the creator function of the corresponding device.
#'@param close_device Whether to close the graphics device after plotting
#' the layout and a 'fileout' has been specified. This is useful to avoid
#' closing the device when saving the layout into a file and willing to add
#' extra elements or figures. Takes TRUE by default. Disregarded if no
#' 'fileout' has been specified.
#'
#'@return
#'\item{brks}{
#' Breaks used for colouring the map (and legend if drawleg = TRUE).
#'}
#'\item{cols}{
#' Colours used for colouring the map (and legend if drawleg = TRUE).
#' Always of length length(brks) - 1.
#'}
#'\item{col_inf}{
#' Colour used to draw the lower triangle end in the colour bar
#' (NULL if not drawn at all).
#'}
#'\item{col_sup}{
#' Colour used to draw the upper triangle end in the colour bar
#' (NULL if not drawn at all).
#'}
#'\item{layout_matrix}{
#' Underlying matrix of the layout. Useful to later set any of the layout
#' cells as current figure to add plot elements. See .SwitchToFigure.
#'}
#'
#'@keywords dynamic
#'@author History:\cr
#' 0.1 - 2016-08 (N. Manubens) - Original code
#'@examples
#'# See examples on Load() to understand the first lines in this example
#' \dontrun{
#'data_path <- system.file('sample_data', package = 's2dverification')
#'expA <- list(name = 'experiment', path = file.path(data_path,
#' 'model/$EXP_NAME$/$STORE_FREQ$_mean/$VAR_NAME$_3hourly',
#' '$VAR_NAME$_$START_DATE$.nc'))
#'obsX <- list(name = 'observation', path = file.path(data_path,
#' '$OBS_NAME$/$STORE_FREQ$_mean/$VAR_NAME$',
#' '$VAR_NAME$_$YEAR$$MONTH$.nc'))
#'
#'# Now we are ready to use Load().
#'startDates <- c('19851101', '19901101', '19951101', '20001101', '20051101')
#'sampleData <- Load('tos', list(expA), list(obsX), startDates,
#' leadtimemin = 1, leadtimemax = 4, output = 'lonlat',
#' latmin = 27, latmax = 48, lonmin = -12, lonmax = 40)
#' }
#' \dontshow{
#'startDates <- c('19851101', '19901101', '19951101', '20001101', '20051101')
#'sampleData <- s2dverification:::.LoadSampleData('tos', c('experiment'),
#' c('observation'), startDates,
#' leadtimemin = 1,
#' leadtimemax = 4,
#' output = 'lonlat',
#' latmin = 27, latmax = 48,
#' lonmin = -12, lonmax = 40)
#' }
#'PlotLayout(PlotEquiMap, c('lat', 'lon'), sampleData$mod[1, , 1, 1, , ],
#' sampleData$lon, sampleData$lat,
#' toptitle = 'Predicted tos for Nov 1960 from 1st Nov',
#' titles = paste('Member', 1:15))
#'
#'@importFrom grDevices dev.cur dev.new dev.off
#'@export
PlotLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
nrow = NULL, ncol = NULL, toptitle = NULL,
row_titles = NULL, col_titles = NULL, bar_scale = 1,
title_scale = 1, title_margin_scale = 1,
title_left_shift_scale = 1,
subtitle_scale = 1, subtitle_margin_scale = 1,
brks = NULL, cols = NULL, drawleg = 'S', titles = NULL,
subsampleg = NULL, bar_limits = NULL,
triangle_ends = NULL, col_inf = NULL, col_sup = NULL,
color_fun = clim.colors,
draw_bar_ticks = TRUE, draw_separators = FALSE,
triangle_ends_scale = 1, bar_extra_labels = NULL,
units = NULL, units_scale = 1, bar_label_scale = 1,
bar_tick_scale = 1, bar_extra_margin = rep(0, 4),
bar_left_shift_scale = 1, bar_label_digits = 4,
extra_margin = rep(0, 4),
fileout = NULL, width = NULL, height = NULL,
size_units = 'in', res = 100, close_device = TRUE) {
# 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
}
is_single_na <- function(x) ifelse(length(x) > 1, FALSE, is.na(x))
# Check var
if (is.array(var) || (is_single_na(var))) {
var <- list(var)
} else if (is.list(var)) {
if (!all(sapply(var, is.array) | sapply(var, is_single_na))) {
stop("Parameter 'var' must be an array or a list of arrays (or NA values).")
}
} else {
stop("Parameter 'var' must be an array or a list of arrays.")
}
# Check fun
if (length(fun) == 1) {
if (is.function(fun)) {
fun <- as.character(substitute(fun))
}
if (is.character(fun)) {
fun <- rep(fun, length(var))
}
}
if (!is.character(fun) || (length(fun) != length(var))) {
stop("Parameter 'fun' must be a single function or a vector of function names, one for each array provided in parameter 'var'.")
}
# Check special_args
if (!is.null(special_args)) {
if (!is.list(special_args) || any(!sapply(special_args, is.list))) {
stop("Parameter 'special_args' must be a list of lists.")
} else if (length(special_args) != length(var)) {
stop("Parameter 'special_args' must contain a list of special arguments for each array provided in 'var'.")
}
}
# Check plot_dims
if (is.character(plot_dims) || is.numeric(plot_dims)) {
plot_dims <- replicate(length(var), plot_dims, simplify = FALSE)
}
if (!is.list(plot_dims) || !all(sapply(plot_dims, is.character) | sapply(plot_dims, is.numeric)) ||
(length(plot_dims) != length(var))) {
stop("Parameter 'plot_dims' must contain a single numeric or character vector with dimension identifiers or a vector for each array provided in parameter 'var'.")
}
# Check nrow
if (!is.null(nrow)) {
if (!is.numeric(nrow)) {
stop("Parameter 'nrow' must be numeric or NULL.")
}
nrow <- round(nrow)
}
# Check ncol
if (!is.null(ncol)) {
if (!is.numeric(ncol)) {
stop("Parameter 'ncol' must be numeric or NULL.")
}
ncol <- round(ncol)
}
# Check toptitle
if (is.null(toptitle) || is.na(toptitle)) {
toptitle <- ''
}
if (!is.character(toptitle)) {
stop("Parameter 'toptitle' must be a character string.")
}
# Check row_titles
if (!is.null(row_titles)) {
if (!is.character(row_titles)) {
stop("Parameter 'row_titles' must be a vector of character strings.")
}
}
# Check col_titles
if (!is.null(row_titles)) {
if (!is.character(row_titles)) {
stop("Parameter 'row_titles' must be a vector of character strings.")
}
}
# Check drawleg
if (is.character(drawleg)) {
if (drawleg %in% c('up', 'u', 'U', 'top', 't', 'T', 'north', 'n', 'N')) {
drawleg <- 'N'
} else if (drawleg %in% c('down', 'd', 'D', 'bottom', 'b', 'B', 'south', 's', 'S')) {
drawleg <- 'S'
} else if (drawleg %in% c('right', 'r', 'R', 'east', 'e', 'E')) {
drawleg <- 'E'
} else if (drawleg %in% c('left', 'l', 'L', 'west', 'w', 'W')) {
drawleg <- 'W'
} else {
stop("Parameter 'drawleg' must be either TRUE, FALSE or a valid identifier of a position (see ?PlotMultiMap).")
}
} else if (!is.logical(drawleg)) {
stop("Parameter 'drawleg' must be either TRUE, FALSE or a valid identifier of a position (see ?PlotMultiMap).")
}
if (drawleg != FALSE && all(sapply(var, is_single_na)) &&
(is.null(brks) || length(brks) < 2)) {
stop("Either data arrays in 'var' or breaks in 'brks' must be provided if 'drawleg' is requested.")
}
# Check the rest of parameters (unless the user simply wants to build an empty layout)
var_limits <- NULL
if (!all(sapply(var, is_single_na))) {
var_limits <- c(min(unlist(var), na.rm = TRUE), max(unlist(var), na.rm = TRUE))
if ((any(is.infinite(var_limits)) || var_limits[1] == var_limits[2])) {
stop("Arrays in parameter 'var' must contain at least 2 different values.")
}
}
colorbar <- ColorBar(brks, cols, FALSE, subsampleg, bar_limits,
var_limits, triangle_ends, col_inf, col_sup, color_fun,
plot = FALSE, draw_bar_ticks,
draw_separators, triangle_ends_scale, bar_extra_labels,
units, units_scale, bar_label_scale, bar_tick_scale,
bar_extra_margin, bar_label_digits)
# Check bar_scale
if (!is.numeric(bar_scale)) {
stop("Parameter 'bar_scale' must be numeric.")
}
# Check bar_left_shift_scale
if (!is.numeric(bar_left_shift_scale)) {
stop("Parameter 'bar_left_shift_scale' must be numeric.")
}
# Check title_scale
if (!is.numeric(title_scale)) {
stop("Parameter 'title_scale' must be numeric.")
}
# Check title_margin_scale
if (!is.numeric(title_margin_scale)) {
stop("Parameter 'title_margin_scale' must be numeric.")
}
# Check title_left_shift_scale
if (!is.numeric(title_left_shift_scale)) {
stop("Parameter 'title_left_shift_scale' must be numeric.")
}
# Check subtitle_scale
if (!is.numeric(subtitle_scale)) {
stop("Parameter 'subtite_scale' must be numeric.")
}
# Check subtitle_margin_scale
if (!is.numeric(subtitle_margin_scale)) {
stop("Parameter 'subtite_margin_scale' must be numeric.")
}
# Check titles
if (!all(sapply(titles, is.character))) {
stop("Parameter 'titles' must be a vector of character strings.")
}
# Check extra_margin
if (!is.numeric(extra_margin) || length(extra_margin) != 4) {
stop("Parameter 'extra_margin' must be a numeric vector with 4 elements.")
}
# Check width
if (is.null(width)) {
if (is.null(fileout)) {
width <- 7
} else {
width <- 11
}
}
if (!is.numeric(width)) {
stop("Parameter 'width' must be numeric.")
}
# Check height
if (is.null(height)) {
if (is.null(fileout)) {
height <- 7
} else {
height <- 8
}
}
if (!is.numeric(height)) {
stop("Parameter 'height' must be numeric.")
}
# Check close_device
if (!is.logical(close_device)) {
stop("Parameter 'close_device' must be logical.")
}
# Count the total number of maps and reorder each array of maps to have the lat and lon dimensions at the end.
n_plots <- 0
plot_array_i <- 1
for (plot_array in var) {
if (is_single_na(plot_array)) {
n_plots <- n_plots + 1
} else {
dim_ids <- plot_dims[[plot_array_i]]
if (is.character(dim_ids)) {
dimnames <- NULL
if (!is.null(names(dim(plot_array)))) {
dimnames <- names(dim(plot_array))
} else if (!is.null(attr(plot_array, 'dimensions'))) {
dimnames <- attr(plot_array, 'dimensions')
}
if (!is.null(dimnames)) {
if (any(!sapply(dim_ids, `%in%`, dimnames))) {
stop("All arrays provided in parameter 'var' must have all the dimensions in 'plot_dims'.")
}
dim_ids <- sapply(dim_ids, function(x) which(dimnames == x)[1])
var[[plot_array_i]] <- .aperm2(var[[plot_array_i]], c((1:length(dim(plot_array)))[-dim_ids], dim_ids))
} else {
.warning(paste0("Assuming the ", plot_array_i, "th array provided in 'var' has 'plot_dims' as last dimensions (right-most)."))
dims <- tail(c(rep(1, length(dim_ids)), dim(plot_array)), length(dim_ids))
dim_ids <- tail(1:length(dim(plot_array)), length(dim_ids))
if (length(dim(var[[plot_array_i]])) < length(dims)) {
dim(var[[plot_array_i]]) <- dims
}
}
} else if (any(dim_ids > length(dim(plot_array)))) {
stop("Parameter 'plot_dims' contains dimension identifiers out of range.")
}
n_plots <- n_plots + prod(dim(plot_array)[-dim_ids])
#n_plots <- n_plots + prod(head(c(rep(1, length(dim_ids)), dim(plot_array)), length(dim(plot_array))))
if (length(dim(var[[plot_array_i]])) == length(dim_ids)) {
dim(var[[plot_array_i]]) <- c(1, dim(var[[plot_array_i]]))
dim_ids <- dim_ids + 1
}
plot_dims[[plot_array_i]] <- dim_ids
}
plot_array_i <- plot_array_i + 1
}
if (is.null(nrow) && is.null(ncol)) {
ncol <- ceiling(sqrt(n_plots))
nrow <- ceiling(n_plots/ncol)
} else if (is.null(ncol)) {
ncol <- ceiling(n_plots/nrow)
} else if (is.null(nrow)) {
nrow <- ceiling(n_plots/ncol)
} else if (nrow * ncol < n_plots) {
stop("There are more arrays to plot in 'var' than cells defined by 'nrow' x 'ncol'.")
}
if (is.logical(drawleg) && drawleg) {
if (nrow > ncol) {
drawleg <- 'S'
} else {
drawleg <- 'E'
}
}
vertical <- drawleg %in% c('E', 'W')
# 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)
} else if (prod(par('mfrow')) > 1) {
dev.new(units = units, res = res, width = width, height = height)
}
# Take size of device and set up layout:
# ---------------------------------------------
# |0000000000000000000000000000000000000000000|
# |0000000000000000 TOP TITLE 0000000000000000|
# |0000000000000000000000000000000000000000000|
# |-------------------------------------------|
# |00000|0000000000000000000000000000000000000|
# |00000|000000000000 ROW TITLES 0000000000000|
# |00000|0000000000000000000000000000000000000|
# |00000|-------------------------------------|
# |0 0|222222222222222222|333333333333333333|
# |0 C 0|222222222222222222|333333333333333333|
# |0 O 0|222222222222222222|333333333333333333|
# |0 L 0|2222 FIGURE 1 2222|3333 FIGURE 2 3333|
# |0 0|222222222222222222|333333333333333333|
# |0 T 0|222222222222222222|333333333333333333|
# |0 I 0|222222222222222222|333333333333333333|
# |0 T 0|-------------------------------------|
# |0 L 0|444444444444444444|555555555555555555|
# |0 S 0|444444444444444444|555555555555555555|
# |0 0|444444444444444444|555555555555555555|
# |00000|4444 FIGURE 3 4444|5555 FIGURE 4 5555|
# |00000|444444444444444444|555555555555555555|
# |00000|444444444444444444|555555555555555555|
# |00000|444444444444444444|555555555555555555|
# |-------------------------------------------|
# |1111111111111111111111111111111111111111111|
# |1111111111111111 COLOR BAR 1111111111111111|
# |1111111111111111111111111111111111111111111|
# ---------------------------------------------
device_size <- par('din')
device_size[1] <- device_size[1] - sum(extra_margin[c(2, 4)])
device_size[2] <- device_size[2] - sum(extra_margin[c(1, 3)])
cs <- char_size <- par('csi')
title_cex <- 2.5 * title_scale
title_margin <- 0.5 * title_cex * title_margin_scale
subtitle_cex <- 1.5 * subtitle_scale
subtitle_margin <- 0.5 * sqrt(nrow * ncol) * subtitle_cex * subtitle_margin_scale
mat_layout <- 1:(nrow * ncol) + ifelse(drawleg != FALSE, 1, 0)
mat_layout <- matrix(mat_layout, nrow, ncol, byrow = TRUE)
fsu <- figure_size_units <- 10 # unitless
widths <- rep(fsu, ncol)
heights <- rep(fsu, nrow)
n_figures <- nrow * ncol
if (length(row_titles) > 0) {
mat_layout <- cbind(rep(0, dim(mat_layout)[1]), mat_layout)
widths <- c(((subtitle_cex + subtitle_margin / 2) * cs / device_size[1]) * ncol * fsu, widths)
}
if (length(col_titles) > 0) {
mat_layout <- rbind(rep(0, dim(mat_layout)[2]), mat_layout)
heights <- c(((subtitle_cex + subtitle_margin) * cs / device_size[2]) * nrow * fsu, heights)
}
if (drawleg != FALSE) {
if (drawleg == 'N') {
mat_layout <- rbind(rep(1, dim(mat_layout)[2]), mat_layout)
heights <- c(round(bar_scale * 2 * nrow), heights)
} else if (drawleg == 'S') {
mat_layout <- rbind(mat_layout, rep(1, dim(mat_layout)[2]))
heights <- c(heights, round(bar_scale * 2 * nrow))
} else if (drawleg == 'W') {
mat_layout <- cbind(rep(1, dim(mat_layout)[1]), mat_layout)
widths <- c(round(bar_scale * 3 * ncol), widths)
} else if (drawleg == 'E') {
mat_layout <- cbind(mat_layout, rep(1, dim(mat_layout)[1]))
widths <- c(widths, round(bar_scale * 3 * ncol))
}
n_figures <- n_figures + 1
}
if (toptitle != '') {
mat_layout <- rbind(rep(0, dim(mat_layout)[2]), mat_layout)
heights <- c(((title_cex + title_margin) * cs / device_size[2]) * nrow * fsu, heights)
}
par(oma = extra_margin)
layout(mat_layout, widths, heights)
# Draw the color bar
if (drawleg != FALSE) {
if (length(row_titles) > 0) {
bar_extra_margin[2] <- bar_extra_margin[2] + (subtitle_cex + subtitle_margin / 2) *
bar_left_shift_scale
}
ColorBar(colorbar$brks, colorbar$cols, vertical, subsampleg,
bar_limits, var_limits,
triangle_ends = triangle_ends, col_inf = colorbar$col_inf,
col_sup = colorbar$col_sup, color_fun, plot = TRUE, draw_bar_ticks,
draw_separators, triangle_ends_scale, bar_extra_labels,
units, units_scale, bar_label_scale, bar_tick_scale,
bar_extra_margin, bar_label_digits)
}
# Draw titles
if (toptitle != '' || length(col_titles) > 0 || length(row_titles) > 0) {
plot(0, type = 'n', ann = FALSE, axes = FALSE, xaxs = 'i', yaxs = 'i',
xlim = c(0, 1), ylim = c(0, 1))
width_lines <- par('fin')[1] / par('csi')
plot_lines <- par('pin')[1] / par('csi')
plot_range <- par('xaxp')[2] - par('xaxp')[1]
size_units_per_line <- plot_range / plot_lines
if (toptitle != '') {
title_x_center <- par('xaxp')[1] - par('mar')[2] * size_units_per_line +
ncol * width_lines * size_units_per_line / 2
if (length(row_titles) > 0) {
title_x_center <- title_x_center - (1 - title_left_shift_scale) *
(subtitle_cex + subtitle_margin) / 2 * size_units_per_line
}
title_y_center <- par('mar')[3] + (title_margin + title_cex) / 2
if (length(col_titles > 0)) {
title_y_center <- title_y_center + (subtitle_margin + subtitle_cex)
}
mtext(toptitle, cex = title_cex, line = title_y_center, at = title_x_center,
padj = 0.5)
}
if (length(col_titles) > 0) {
t_x_center <- par('xaxp')[1] - par('mar')[2] * size_units_per_line
for (t in 1:ncol) {
mtext(col_titles[t], cex = subtitle_cex,
line = par('mar')[3] + (subtitle_margin + subtitle_cex) / 2,
at = t_x_center + (t - 0.5) * width_lines * size_units_per_line,
padj = 0.5)
}
}
height_lines <- par('fin')[2] / par('csi')
plot_lines <- par('pin')[2] / par('csi')
plot_range <- par('yaxp')[2] - par('yaxp')[1]
size_units_per_line <- plot_range / plot_lines
if (length(row_titles) > 0) {
t_y_center <- par('yaxp')[1] - par('mar')[1] * size_units_per_line
for (t in 1:nrow) {
mtext(row_titles[t], cex = subtitle_cex,
line = par('mar')[2] + (subtitle_margin + subtitle_cex) / 2,
at = t_y_center - (t - 1.5) * height_lines * size_units_per_line,
padj = 0.5, side = 2)
}
}
par(new = TRUE)
}
array_number <- 1
plot_number <- 1
# For each array provided in var
lapply(var, function(x) {
if (is_single_na(x)) {
if (!all(sapply(var[array_number:length(var)], is_single_na))) {
plot.new()
par(new = FALSE)
}
plot_number <<- plot_number + 1
} else {
if (is.character(plot_dims[[array_number]])) {
plot_dim_indices <- which(names(dim(x)) %in% plot_dims[[array_number]])
} else {
plot_dim_indices <- plot_dims[[array_number]]
}
# For each of the arrays provided in that array
apply(x, (1:length(dim(x)))[-plot_dim_indices],
function(y) {
# Do the plot
fun_args <- c(list(y, toptitle = titles[plot_number]), list(...),
special_args[[array_number]])
funct <- fun[[array_number]]
if (fun[[array_number]] %in% c('PlotEquiMap', 'PlotStereoMap', 'PlotSection')) {
fun_args <- c(fun_args, list(brks = colorbar$brks, cols = colorbar$cols,
col_inf = colorbar$col_inf,
col_sup = colorbar$col_sup,
drawleg = FALSE))
}
do.call(fun[[array_number]], fun_args)
plot_number <<- plot_number + 1
})
}
array_number <<- array_number + 1
})
# If the graphic was saved to file, close the connection with the device
if (!is.null(fileout) && close_device) dev.off()
invisible(list(brks = colorbar$brks, cols = colorbar$cols,
col_inf = colorbar$col_inf, col_sup = colorbar$col_sup,
layout_matrix = mat_layout))
}
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