From 22cc3ac7875ca779487c0ab3f3f119c1446f1309 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 25 Jun 2025 12:24:36 +0200
Subject: [PATCH 1/4] Update ColorBarContinuous.R to match esviz version

---
 .../Visualization/R/tmp/ColorBarContinuous.R  | 197 ++++++++++--------
 1 file changed, 112 insertions(+), 85 deletions(-)

diff --git a/modules/Visualization/R/tmp/ColorBarContinuous.R b/modules/Visualization/R/tmp/ColorBarContinuous.R
index b7727ba0..ccbb634a 100644
--- a/modules/Visualization/R/tmp/ColorBarContinuous.R
+++ b/modules/Visualization/R/tmp/ColorBarContinuous.R
@@ -45,7 +45,7 @@
 #'  colorbar. Takes by default an approximation of a value that yields a 
 #'  readable tick arrangement (extreme breaks always ticked). If set to 0 or 
 #'  lower, no labels are drawn. See the code of the function for details or 
-#'  use 'extra_labels' for customized tick arrangements.
+#'  use 'bar_extra_labels' for customized tick arrangements.
 #'@param bar_limits Vector of two numeric values with the extremes of the 
 #'  range of values represented in the colour bar. If 'var_limits' go beyond 
 #'  this interval, the drawing of triangle extremes is triggered at the 
@@ -82,7 +82,7 @@
 #'  parameter is set by default to ClimPalette().
 #'@param plot Logical value indicating whether to only compute its breaks and 
 #'  colours (FALSE) or to also draw it on the current device (TRUE).
-#'@param draw_ticks Whether to draw ticks for the labels along the colour bar 
+#'@param draw_bar_ticks Whether to draw ticks for the labels along the colour bar 
 #' (TRUE) or not (FALSE). TRUE by default. Disregarded if 'plot = FALSE'.
 #'@param draw_separators Whether to draw black lines in the borders of each of 
 #'  the colour rectancles of the colour bar (TRUE) or not (FALSE). FALSE by 
@@ -91,24 +91,29 @@
 #'  colour bar, if drawn at all. Takes 1 by default (rectangle triangle 
 #'  proportional to the thickness of the colour bar). Disregarded if 
 #'  'plot = FALSE'.
-#'@param extra_labels Numeric vector of extra labels to draw along axis of 
+#'@param bar_extra_labels Numeric vector of extra labels to draw along axis of 
 #'  the colour bar. The number of provided decimals will be conserved. 
 #'  Disregarded if 'plot = FALSE'.
+#'@param extra_labels Deprecated. Use 'bar_extra_labels' instead.
 #'@param title Title to draw on top of the colour bar, most commonly with the 
 #'  units of the represented field in the neighbour figures. Empty by default.
 #'@param title_scale Scale factor for the 'title' of the colour bar. 
 #'  Takes 1 by default.
-#'@param label_scale Scale factor for the labels of the colour bar. 
+#'@param bar_label_scale Scale factor for the labels of the colour bar. 
 #'  Takes 1 by default.
-#'@param tick_scale Scale factor for the length of the ticks of the labels 
+#'@param label_scale Deprecated. Use 'bar_label_scale' instead.
+#'@param bar_tick_scale Scale factor for the length of the ticks of the labels 
 #'  along the colour bar. Takes 1 by default.
-#'@param extra_margin Extra margins to be added around the colour bar, 
+#'@param tick_scale Deprecated. Use 'bar_tick_scale' instead.
+#'@param bar_extra_margin Extra margins to be added around the colour bar, 
 #'  in the format c(y1, x1, y2, x2). The units are margin lines. Takes 
 #'  rep(0, 4) by default.
-#'@param label_digits Number of significant digits to be displayed in the 
+#'@param extra_margin Deprecated. Use 'bar_extra_margin' instead.
+#'@param bar_label_digits Number of significant digits to be displayed in the 
 #'  labels of the colour bar, usually to avoid too many decimal digits 
 #'  overflowing the figure region. This does not have effect over the labels 
-#'  provided in 'extra_labels'. Takes 4 by default.
+#'  provided in 'bar_extra_labels'. Takes 4 by default.
+#'@param label_digits Deprecated. Use 'bar_label_digits' instead.
 #'@param ... Arguments to be passed to the method. Only accepts the following 
 #'  graphical parameters:\cr adj ann ask bg bty cex.lab cex.main cex.sub cin 
 #'  col.axis col.lab col.main col.sub cra crt csi cxy err family fg fig fin 
@@ -144,20 +149,22 @@
 #'@import utils
 #'@export
 ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE, 
-                     subsampleg = NULL, bar_limits = NULL, var_limits = NULL, 
-                     triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
-                     color_fun = ClimPalette(), plot = TRUE, 
-                     draw_ticks = TRUE, draw_separators = FALSE, 
-                     triangle_ends_scale = 1, extra_labels = NULL, 
-                     title = NULL, title_scale = 1, 
-                     label_scale = 1, tick_scale = 1, 
-                     extra_margin = rep(0, 4), label_digits = 4, ...) {
+                               subsampleg = NULL, bar_limits = NULL, var_limits = NULL, 
+                               triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
+                               color_fun = ClimPalette(), plot = TRUE, 
+                               draw_bar_ticks = TRUE, draw_separators = FALSE, 
+                               triangle_ends_scale = 1, bar_extra_labels = NULL,
+                               extra_labels = NULL, title = NULL, title_scale = 1, 
+                               bar_label_scale = 1, label_scale = NULL,
+                               bar_tick_scale = 1, tick_scale = NULL,
+                               bar_extra_margin = rep(0, 4), extra_margin = NULL,
+                               bar_label_digits = 4, label_digits = NULL, ...) {
   # Required checks
   if ((is.null(brks) || length(brks) < 2) && is.null(bar_limits) && is.null(var_limits)) {
     stop("At least one of 'brks' with the desired breaks, 'bar_limits' or ",
          "'var_limits' must be provided to generate the colour bar.")
   }
-
+  
   # Check brks
   if (!is.null(brks)) {
     if (!is.numeric(brks)) {
@@ -170,14 +177,14 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
       brks <- reorder$x
     } 
   }
-
+  
   # Check bar_limits
   if (!is.null(bar_limits)) {
     if (!(all(is.na(bar_limits) | is.numeric(bar_limits)) && (length(bar_limits) == 2))) {
       stop("Parameter 'bar_limits' must be a vector of two numeric elements or NAs.")
     }
   }
-
+  
   # Check var_limits
   if (!is.null(var_limits)) {
     if (!(is.numeric(var_limits) && (length(var_limits) == 2))) {
@@ -188,7 +195,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
       stop("Parameter 'var_limits' must not contain infinite values.")
     }
   }
-
+  
   # Check cols
   if (!is.null(cols)) {
     if (!is.character(cols)) {
@@ -197,12 +204,12 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
       stop("Parameter 'cols' must contain valid colour identifiers.")
     }
   }
-
+  
   # Check color_fun
   if (!is.function(color_fun)) {
     stop("Parameter 'color_fun' must be a colour-generator function.")
   }
-
+  
   # Check integrity among brks, bar_limits and var_limits
   if (is.null(brks) || (length(brks) < 2)) {
     if (is.null(brks)) {
@@ -249,21 +256,21 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
       stop("Parameters 'brks' and 'bar_limits' are inconsistent.")
     }
   }
-
+  
   # Check col_inf
   if (!is.null(col_inf)) {
     if (!.IsColor(col_inf)) {
       stop("Parameter 'col_inf' must be a valid colour identifier.")
     }
   }  
-
+  
   # Check col_sup
   if (!is.null(col_sup)) {
     if (!.IsColor(col_sup)) {
       stop("Parameter 'col_sup' must be a valid colour identifier.")
     }
   }
-
+  
   # Check triangle_ends
   if (!is.null(triangle_ends) && (!is.logical(triangle_ends) || length(triangle_ends) != 2)) {
     stop("Parameter 'triangle_ends' must be a logical vector with two elements.")
@@ -293,16 +300,16 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
   if (plot && !is.null(var_limits)) {
     if ((bar_limits[1] > var_limits[1]) && !triangle_ends[1]) {
       warning("There are variable values smaller than the lower limit ",
-               "of the colour bar and the lower triangle end has been ",
-               "disabled. These will be painted in the colour for NA values.")
+              "of the colour bar and the lower triangle end has been ",
+              "disabled. These will be painted in the colour for NA values.")
     }
     if ((bar_limits[2] < var_limits[2]) && !triangle_ends[2]) {
       warning("There are variable values greater than the higher limit ",
-               "of the colour bar and the higher triangle end has been ",
-               "disabled. These will be painted in the colour for NA values.")
+              "of the colour bar and the higher triangle end has been ",
+              "disabled. These will be painted in the colour for NA values.")
     }
   }
-
+  
   # Generate colours if needed
   if (is.null(cols)) {
     cols <- color_fun(length(brks) - 1 + sum(triangle_ends))
@@ -319,25 +326,29 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
   } else if ((length(cols) != (length(brks) - 1))) {
     stop("Incorrect number of 'brks' and 'cols'. There must be one more break than the number of colours.")
   }
-
+  
   # Check vertical
   if (!is.logical(vertical)) {
     stop("Parameter 'vertical' must be TRUE or FALSE.")
   }
-
-  # Check extra_labels
-  if (is.null(extra_labels)) {
-    extra_labels <- numeric(0)
+  
+  # Check bar_extra_labels
+  if (missing(bar_extra_labels) && !missing(extra_labels)) {
+    warning("The parameter 'extra_labels' is deprecated. Use 'bar_extra_labels' instead.")
+    bar_extra_labels <- extra_labels
   }
-  if (!is.numeric(extra_labels)) {
-    stop("Parameter 'extra_labels' must be numeric.")
+  if (is.null(bar_extra_labels)) {
+    bar_extra_labels <- numeric(0)
+  }
+  if (!is.numeric(bar_extra_labels)) {
+    stop("Parameter 'bar_extra_labels' must be numeric.")
   } else {
-    if (any(extra_labels > bar_limits[2]) || any(extra_labels < bar_limits[1])) {
-      stop("Parameter 'extra_labels' must not contain ticks beyond the color bar limits.")
+    if (any(bar_extra_labels > bar_limits[2]) || any(bar_extra_labels < bar_limits[1])) {
+      stop("Parameter 'bar_extra_labels' must not contain ticks beyond the color bar limits.")
     }
   }
-  extra_labels <- sort(extra_labels)
-
+  bar_extra_labels <- sort(bar_extra_labels)
+  
   # Check subsampleg
   primes <- function(x) {
     # Courtesy of Chase. See http://stackoverflow.com/questions/6424856/r-function-for-returning-all-factors
@@ -358,7 +369,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     }
     if (subsampleg > (length(brks) - 1) / 4) {
       subsampleg <- max(1, round(length(brks) / 4))
-      extra_labels <- c(extra_labels, bar_limits[2])
+      bar_extra_labels <- c(bar_extra_labels, bar_limits[2])
       added_final_tick <- TRUE
       if ((length(brks) - 1) %% subsampleg < (length(brks) - 1) / 4 / 2) {
         remove_final_tick <- TRUE
@@ -372,27 +383,27 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
   if ((subsampleg) < 1) {
     draw_labels <- FALSE
   }
-
+  
   # Check plot
   if (!is.logical(plot)) {
     stop("Parameter 'plot' must be logical.")
   }
-
+  
   # Check draw_separators
   if (!is.logical(draw_separators)) {
     stop("Parameter 'draw_separators' must be logical.")
   }
-
+  
   # Check triangle_ends_scale
   if (!is.numeric(triangle_ends_scale)) {
     stop("Parameter 'triangle_ends_scale' must be numeric.")
   }
-
-  # Check draw_ticks
-  if (!is.logical(draw_ticks)) {
-    stop("Parameter 'draw_ticks' must be logical.")
+  
+  # Check draw_bar_ticks
+  if (!is.logical(draw_bar_ticks)) {
+    stop("Parameter 'draw_bar_ticks' must be logical.")
   }
-
+  
   # Check title
   if (is.null(title)) {
     title <- ''
@@ -400,38 +411,54 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
   if (!is.character(title)) {
     stop("Parameter 'title' must be a character string.")
   }
-
+  
   # Check title_scale
   if (!is.numeric(title_scale)) {
     stop("Parameter 'title_scale' must be numeric.")
   }
-
-  # Check label_scale
-  if (!is.numeric(label_scale)) {
-    stop("Parameter 'label_scale' must be numeric.")
+  
+  # Check bar_label_scale
+  if (missing(bar_label_scale) && !missing(label_scale)) {
+    warning("The parameter 'label_scale' is deprecated. Use 'bar_label_scale' instead.")
+    bar_label_scale <- label_scale
+  }
+  if (!is.numeric(bar_label_scale)) {
+    stop("Parameter 'bar_label_scale' must be numeric.")
+  }
+  
+  # Check bar_tick_scale
+  if (missing(bar_tick_scale) && !missing(tick_scale)) {
+    warning("The parameter 'tick_scale' is deprecated. Use 'bar_tick_scale' instead.")
+    bar_tick_scale <- tick_scale
+  }
+  if (!is.numeric(bar_tick_scale)) {
+    stop("Parameter 'bar_tick_scale' must be numeric.")
+  }
+  
+  # Check bar_extra_margin
+  if (missing(bar_extra_margin) && !missing(extra_margin)) {
+    warning("The parameter 'extra_margin' is deprecated. Use 'bar_extra_margin' instead.")
+    bar_extra_margin <- extra_margin
   }
-
-  # Check tick_scale
-  if (!is.numeric(tick_scale)) {
-    stop("Parameter 'tick_scale' must be numeric.")
+  if (!is.numeric(bar_extra_margin) || length(bar_extra_margin) != 4) {
+    stop("Parameter 'bar_extra_margin' must be a numeric vector of length 4.")
   }
-
-  # Check extra_margin
-  if (!is.numeric(extra_margin) || length(extra_margin) != 4) {
-    stop("Parameter 'extra_margin' must be a numeric vector of length 4.")
+  
+  # Check bar_label_digits
+  if (missing(bar_label_digits) && !missing(label_digits)) {
+    warning("The parameter 'label_digits' is deprecated. Use 'bar_label_digits' instead.")
+    bar_label_digits <- label_digits
   }
-
-  # Check label_digits
-  if (!is.numeric(label_digits)) {
-    stop("Parameter 'label_digits' must be numeric.")
+  if (!is.numeric(bar_label_digits)) {
+    stop("Parameter 'bar_label_digits' must be numeric.")
   }
-  label_digits <- round(label_digits)
-
+  bar_label_digits <- round(bar_label_digits)
+  
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "col", "lab", "las", "mar", "mgp", "new", "ps")
   userArgs <- .FilterUserGraphicArgs(excludedArgs, ...)
-
+  
   #
   #  Plotting colorbar
   # ~~~~~~~~~~~~~~~~~~~
@@ -448,29 +475,29 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     if (vertical) {
       figure_size <- rev(figure_size)
     }
-#    pannel_to_redraw <- par('mfg')
-#    .SwitchToFigure(pannel_to_redraw[1], pannel_to_redraw[2])
+    #    pannel_to_redraw <- par('mfg')
+    #    .SwitchToFigure(pannel_to_redraw[1], pannel_to_redraw[2])
     # Load the user parameters
     par(new = TRUE)
     par(userArgs)
     # Set up color bar plot region
     margins <- c(0.0, 0, 0.0, 0)
     cex_title <- 1 * title_scale
-    cex_labels <- 0.9 * label_scale
-    cex_ticks <- -0.3 * tick_scale
+    cex_labels <- 0.9 * bar_label_scale
+    cex_ticks <- -0.3 * bar_tick_scale
     spaceticklab <- max(-cex_ticks, 0)
     if (vertical) {
       margins[1] <- margins[1] + (1.2 * cex_labels * 3 + spaceticklab) * cs
-      margins <- margins + extra_margin[c(4, 1:3)] * cs
+      margins <- margins + bar_extra_margin[c(4, 1:3)] * cs
     } else {
       margins[1] <- margins[1] + (1.2 * cex_labels * 1 + spaceticklab) * cs
-      margins <- margins + extra_margin * cs
+      margins <- margins + bar_extra_margin * cs
     }
     if (title != '') {
       margins[3] <- margins[3] + (1.0 * cex_title) * cs
     }
     margins[3] <- margins[3] + sqrt(figure_size[2] / (margins[1] + margins[3])) * 
-                               figure_size[2] / 6 * ifelse(title != '', 0.5, 0.8)
+      figure_size[2] / 6 * ifelse(title != '', 0.5, 0.8)
     # Set side margins
     margins[2] <- margins[2] + figure_size[1] / 16
     margins[4] <- margins[4] + figure_size[1] / 16
@@ -511,7 +538,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
       # try and error
       par(mai = margins, 
           mgp = c(0, cex_labels / 2 + spaceticklab 
-                     - cex_labels / 4 * (3 / cex_labels - 1), 0),
+                  - cex_labels / 4 * (3 / cex_labels - 1), 0),
           las = 1)
       d <- 1
       image(1:ncols, 1, t(t(1:ncols)), axes = FALSE, col = cols, 
@@ -535,7 +562,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
       lines(right_triangle$x, right_triangle$y)
     }
     par(xpd = FALSE)
-
+    
     # Put the separators
     if (vertical) {
       if (draw_separators) {
@@ -565,7 +592,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     # Put the ticks
     plot_range <- length(brks) - 1
     var_range <- tail(brks, 1) - head(brks, 1)
-    extra_labels_at <- ((extra_labels - head(brks, 1)) / var_range) * plot_range + 0.5
+    bar_extra_labels_at <- ((bar_extra_labels - head(brks, 1)) / var_range) * plot_range + 0.5
     at <- seq(1, length(brks), subsampleg)
     labels <- brks[at]
     # Getting rid of next-to-last tick if too close to last one
@@ -573,13 +600,13 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
       at <- at[-length(at)]
       labels <- labels[-length(labels)]
     }
-    labels <- signif(labels, label_digits)
+    labels <- signif(labels, bar_label_digits)
     if (added_final_tick) {
-      extra_labels[length(extra_labels)] <- signif(tail(extra_labels, 1), label_digits)
+      bar_extra_labels[length(bar_extra_labels)] <- signif(tail(bar_extra_labels, 1), bar_label_digits)
     }
     at <- at - 0.5
-    at <- c(at, extra_labels_at)
-    labels <- c(labels, extra_labels)
+    at <- c(at, bar_extra_labels_at)
+    labels <- c(labels, bar_extra_labels)
     tick_reorder <- sort(at, index.return = TRUE)
     at <- tick_reorder$x
     if (draw_labels) {
@@ -587,7 +614,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     } else {
       labels <- FALSE
     }
-    axis(d, at = at, tick = draw_ticks, labels = labels, cex.axis = cex_labels, tcl = cex_ticks)
+    axis(d, at = at, tick = draw_bar_ticks, labels = labels, cex.axis = cex_labels, tcl = cex_ticks)
     par(saved_pars)
   }
   invisible(list(brks = brks, cols = cols, col_inf = col_inf, col_sup = col_sup))
-- 
GitLab


From aa4dc5ec3d2f3f08d37e070e3b8f1fed90f3a4b2 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 25 Jun 2025 12:25:30 +0200
Subject: [PATCH 2/4] Update VizEquiMap.R to match esviz version

---
 modules/Visualization/R/tmp/VizEquiMap.R | 261 ++++++++++++-----------
 1 file changed, 135 insertions(+), 126 deletions(-)

diff --git a/modules/Visualization/R/tmp/VizEquiMap.R b/modules/Visualization/R/tmp/VizEquiMap.R
index 6fef1036..f3855901 100644
--- a/modules/Visualization/R/tmp/VizEquiMap.R
+++ b/modules/Visualization/R/tmp/VizEquiMap.R
@@ -10,7 +10,7 @@
 #'include continents, oceans, and lakes. This plot function is compatible with
 #'figure layouts if colour bar is disabled.
 #'
-#'@param var Array with the values at each cell of a grid on a regular 
+#'@param data Array with the values at each cell of a grid on a regular 
 #'  rectangular or gaussian grid. The array is expected to have two 
 #'  dimensions: c(latitude, longitude). Longitudes can be in ascending or 
 #'  descending order and latitudes in any order. It can contain NA values 
@@ -19,20 +19,21 @@
 #'  this alternative is not appropriate for square arrays. It is allowed that
 #'  the positions of the longitudinal and latitudinal coordinate dimensions 
 #'  are interchanged.
+#'@param var Deprecated. Use 'data' instead.
 #'@param lon Numeric vector of longitude locations of the cell centers of the 
-#'  grid of 'var', in ascending or descending order (same as 'var'). Expected 
+#'  grid of 'data', in ascending or descending order (same as 'data'). Expected 
 #'  to be regularly spaced, within either of the ranges [-180, 180] or 
 #'  [0, 360]. Data for two adjacent regions split by the limits of the 
 #'  longitude range can also be provided, e.g. \code{lon = c(0:50, 300:360)} 
-#'  ('var' must be provided consitently).
+#'  ('data' must be provided consitently).
 #'@param lat Numeric vector of latitude locations of the cell centers of the 
-#'  grid of 'var', in any order (same as 'var'). Expected to be from a regular 
+#'  grid of 'data', in any order (same as 'data'). Expected to be from a regular 
 #'  rectangular or gaussian grid, within the range [-90, 90].
 #'@param varu Array of the zonal component of wind/current/other field with 
-#'  the same dimensions as 'var'. It is allowed that the positions of the 
+#'  the same dimensions as 'data'. It is allowed that the positions of the 
 #'  longitudinal and latitudinal coordinate dimensions are interchanged.
 #'@param varv Array of the meridional component of wind/current/other field 
-#'  with the same dimensions as 'var'. It is allowed that the positions of the 
+#'  with the same dimensions as 'data'. It is allowed that the positions of the 
 #'  longitudinal and latitudinal coordinate dimensions are interchanged.
 #'@param toptitle Top title of the figure, scalable with parameter 
 #'  'title_scale'.
@@ -43,18 +44,18 @@
 #'  manipulation functions like \code{paste()} or \code{paste0()}, using 
 #'  \code{"\n"} to indicate line breaks. 
 #'@param units Title at the top of the colour bar, most commonly the units of 
-#'  the variable provided in parameter 'var'.
+#'  the variable provided in parameter 'data'.
 #'@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 
+#'  in 'data'. The corresponding grid cell of a given value in 'data' 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,colNA Colour identifiers to colour the values in 
-#'  'var' that go beyond the extremes of the colour bar and to colour NA 
+#'  'data' that go beyond the extremes of the colour bar and to colour NA 
 #'  values, respectively. 'colNA' takes attr(cols, 'na_color') if available by 
 #'  default, where cols is the parameter 'cols' if provided or the vector of 
 #'  colors returned by 'color_fun'. If not available, it takes 'pink' by 
@@ -70,7 +71,7 @@
 #'  parameters to control the visual aspect of the drawn colour bar (3/3). 
 #'  See ?ColorBar for a full explanation.
 #'@param square Logical value to choose either to draw a coloured square for 
-#'  each grid cell in 'var' (TRUE; default) or to draw contour lines and fill 
+#'  each grid cell in 'data' (TRUE; default) or to draw contour lines and fill 
 #'  the spaces in between with colours (FALSE). In the latter case, 
 #'  'filled.continents' will take the value FALSE if not specified.
 #'@param filled.continents Colour to fill in drawn projected continents. 
@@ -94,7 +95,7 @@
 #'  location of the shape. The default value is NULL.
 #'@param shapefile_color Line color of the shapefile.
 #'@param shapefile_lwd Line width of the shapefile. The default value is 1. 
-#'@param contours Array of same dimensions as 'var' to be added to the plot 
+#'@param contours Array of same dimensions as 'data' to be added to the plot 
 #'  and displayed with contours. Parameter 'brks2' is required to define the 
 #'  magnitude breaks for each contour curve. Disregarded if 'square = FALSE'.
 #'  It is allowed that the positions of the longitudinal and latitudinal 
@@ -111,8 +112,8 @@
 #'  contour labels or not. The default value is TRUE.
 #'@param contour_label_scale Scale factor for the superimposed labels when 
 #'  drawing contour levels.
-#'@param dots Array of same dimensions as 'var' or with dimensions 
-#'  c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
+#'@param dots Array of same dimensions as 'data' or with dimensions 
+#'  c(n, dim(data)), where n is the number of dot/symbol layers to add to the 
 #'  plot. A value of TRUE at a grid cell will draw a dot/symbol on the 
 #'  corresponding square of the plot. By default all layers provided in 'dots' 
 #'  are plotted with dots, but a symbol can be specified for each of the 
@@ -126,7 +127,7 @@
 #'@param dot_size Scale factor for the dots/symbols to be plotted, specified 
 #'  in 'dots'. If a single value is specified, it will be applied to all 
 #'  layers in 'dots'. Takes 1 by default.
-#'@param mask An array with the same dimensions as 'var' of [0, 1] or logical
+#'@param mask An array with the same dimensions as 'data' of [0, 1] or logical
 #'  indicating the grids to not plot data. The value 0 or FALSE is the point not
 #'  to be plotted.
 #'@param mask_color Color of the mask. The default value is 'white'.
@@ -184,6 +185,31 @@
 #'@param vertical TRUE/FALSE for vertical/horizontal colour bar. Default is 
 #'  FALSE. Parameters 'width' and 'height' might need to be modified to
 #'  accommodate the vertical colour bar.
+#'@param include_lower_boundary Logical value indicating whether to include
+#'  the minimum value of the field. Takes TRUE by default.
+#'@param include_upper_boundary Logical value indicating whether to include
+#'  the maximum value of the field. Takes TRUE by default.
+#'@param hatching_mask Logical or binary (0/1) array with two named dimensions:
+#' c(latitude, longitude). Hatching is applied to grid cells where
+#' 'hatching_mask' is TRUE (or 1). Arrays with dimensions c(longitude, latitude)
+#' are also accepted, but the resulting hatching may appear transposed. To
+#' ensure correct alignment with the map, provide 'data'. The function will
+#' compare the dimension order of 'hatching_mask' and 'data', and automatically
+#' transpose 'hatching_mask' if the latitude and longitude dimensions appear to
+#' be reversed.
+#'@param hatching_density The density of shading lines, in lines per inch. A
+#'  zero value of density means no shading nor filling, whereas negative values
+#'  and NA suppress shading (and so allow color filling). NULL means that no
+#'  shading lines are drawn. Default is 10.
+#'@param hatching_angle The slope of shading lines, given as an angle in degrees
+#'  (counter-clockwise). Default is 45.
+#'@param hatching_color Color of the hatching lines. Default is
+#'  \code{"#252525"}.
+#'@param hatching_lwd The line width, a positive number. The interpretation is
+#'  device-specific, and some devices do not implement line widths less than
+#'  one. Default is 0.5.
+#'@param hatching_cross A logical value indicating crosshatching. If TRUE, adds
+#'  a second set of lines in the opposite angle. Default is FALSE.
 #'@param boxlim Limits of a box to be added to the plot, in degrees: 
 #'  c(x1, y1, x2, y2). A list with multiple box specifications can also be 
 #'  provided.
@@ -203,40 +229,15 @@
 #'@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 File width, in the units specified in the parameter size_units 
+#'@param width File width, in the units specified in the parameter 'size_units' 
 #'  (inches by default). Takes 8 by default.
 #'@param height File height, in the units specified in the parameter 
-#'  size_units (inches by default). Takes 5 by default.
+#'  'size_units' (inches by default). Takes 5 by default.
 #'@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 include_lower_boundary Logical value indicating whether to include
-#'  the minimum value of the field. Takes TRUE by default.
-#'@param include_upper_boundary Logical value indicating whether to include
-#'  the maximum value of the field. Takes TRUE by default.
-#'@param hatching_mask Logical or binary (0/1) array with two named dimensions:
-#' c(latitude, longitude). Hatching is applied to grid cells where
-#' 'hatching_mask' is TRUE (or 1). Arrays with dimensions c(longitude, latitude)
-#' are also accepted, but the resulting hatching may appear transposed. To
-#' ensure correct alignment with the map, provide 'data'. The function will
-#' compare the dimension order of 'hatching_mask' and 'data', and automatically
-#' transpose 'hatching_mask' if the latitude and longitude dimensions appear to
-#' be reversed.
-#'@param hatching_density The density of shading lines, in lines per inch. A
-#'  zero value of density means no shading nor filling, whereas negative values
-#'  and NA suppress shading (and so allow color filling). NULL means that no
-#'  shading lines are drawn. Default is 10.
-#'@param hatching_angle The slope of shading lines, given as an angle in degrees
-#'  (counter-clockwise). Default is 45.
-#'@param hatching_color Color of the hatching lines. Default is
-#'  \code{"#252525"}.
-#'@param hatching_lwd The line width, a positive number. The interpretation is
-#'  device-specific, and some devices do not implement line widths less than
-#'  one. Default is 0.5.
-#'@param hatching_cross A logical value indicating crosshatching. If TRUE, adds
-#'  a second set of lines in the opposite angle. Default is FALSE.
 #'@param \dots Arguments to be passed to the method. Only accepts the following 
 #'  graphical parameters:\cr
 #'  adj ann ask bg bty cex.sub cin col.axis col.lab col.main col.sub cra crt 
@@ -266,11 +267,11 @@
 #'  \dontrun{
 #'ano <- s2dv::Ano_CrossValid(map_temp$exp, map_temp$obs, memb = FALSE,
 #'                            dat_dim = c('dat', 'member'), memb_dim = 'member')
-#'var <- s2dv::MeanDims(ano$exp, "member")
+#'data <- s2dv::MeanDims(ano$exp, "member")
 #'lats <- attr(map_temp$exp, "Variables")$common$lat
 #'lons <- attr(map_temp$exp, "Variables")$common$lon
 #'
-#'VizEquiMap(var[1, 1, 1, 1, , ], lon = lons, lat = lats,
+#'VizEquiMap(data[1, 1, 1, 1, , ], lon = lons, lat = lats,
 #'           toptitle = 'Near-surface temperature anomaly, Nov. 2000',
 #'           filled.continents = FALSE, title_scale = 0.7,
 #'           caption = paste0("This is a test caption.", "\n",
@@ -279,9 +280,9 @@
 #'@import graphics maps utils
 #'@importFrom grDevices dev.cur dev.new dev.off gray
 #'@importFrom stats cor
-#' @importFrom s2dv InsertDim
+#'@importFrom s2dv InsertDim
 #'@export
-VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
+VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
                        toptitle = NULL, sizetit = NULL, caption = NULL,
                        units = NULL, brks = NULL, cols = NULL, bar_limits = NULL, 
                        triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
@@ -308,16 +309,17 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
                        draw_separators = FALSE, triangle_ends_scale = 1, 
                        bar_label_digits = 4, bar_label_scale = 1, 
                        units_scale = 1, bar_tick_scale = 1, 
-                       bar_extra_margin = rep(0, 4),
+                       bar_extra_margin = rep(0, 4), 
+                       include_lower_boundary = TRUE,
+                       include_upper_boundary = TRUE, hatching_mask = NULL,
+                       hatching_density = 10, hatching_angle = 45,
+                       hatching_color = "#252525", hatching_lwd = 0.5,
+                       hatching_cross = FALSE,
                        boxlim = NULL, boxcol = 'purple2', boxlwd = 5, 
                        margin_scale = rep(1, 4), title_scale = 1, 
                        caption_size = 0.8, numbfig = NULL, fileout = NULL, 
                        width = 8, height = 5, size_units = 'in', 
-                       res = 100, include_lower_boundary = TRUE,
-                       include_upper_boundary = TRUE, hatching_mask = NULL,
-                       hatching_density = 10, hatching_angle = 45,
-                       hatching_color = "#252525", hatching_lwd = 0.5,
-                       hatching_cross = FALSE, ...) {
+                       res = 100, var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "din", "fig", "fin", "lab", "las", "lty", "lwd", "mai", "mar", "mgp", "new", "oma", "ps", "tck")
@@ -336,59 +338,66 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     stop("Parameters 'lon' and 'lat' must be numeric vectors.")
   }
   
-  # Check var
-  if (is.null(var)) {
-    stop("Parameter 'var' cannot be NULL.")
+  # Check data
+  if (missing(data) || is.null(data)) {
+    if (!is.null(var)) {
+      data <- var
+      warning("The parameter 'var' is deprecated. Use 'data' instead.")
+    } else {
+      stop("Parameter 'data' cannot be NULL.")
+    }
+  } else if (!is.null(var)) {
+    warning("The parameter 'var' is deprecated. 'data' will be used instead.")
   }
-  if (!is.array(var)) {
-    stop("Parameter 'var' must be a numeric array.")
+  if (!is.array(data)) {
+    stop("Parameter 'data' must be a numeric array.")
   }
   
   transpose <- FALSE
-  if (!is.null(names(dim(var)))) {
-    if (any(names(dim(var)) %in% .KnownLonNames()) &&
-        any(names(dim(var)) %in% .KnownLatNames())) {
-      lon_dim <- names(dim(var))[names(dim(var)) %in% .KnownLonNames()]
-      lat_dim <- names(dim(var))[names(dim(var)) %in% .KnownLatNames()]
+  if (!is.null(names(dim(data)))) {
+    if (any(names(dim(data)) %in% .KnownLonNames()) &&
+        any(names(dim(data)) %in% .KnownLatNames())) {
+      lon_dim <- names(dim(data))[names(dim(data)) %in% .KnownLonNames()]
+      lat_dim <- names(dim(data))[names(dim(data)) %in% .KnownLatNames()]
     } else {
-      names(dim(var)) <- NULL
+      names(dim(data)) <- NULL
       lat_dim <- NULL
       lon_dim <- NULL
-      warning("Dimension names of 'var' doesn't correspond to any coordinates names supported by s2dv package.")
+      warning("Dimension names of 'data' doesn't correspond to any coordinates names supported by s2dv package.")
     }
   } else {
     lon_dim <- NULL
     lat_dim <- NULL
-    warning("Parameter 'var' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
+    warning("Parameter 'data' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
   }
   
-  if (length(dim(var)) > 2) {
+  if (length(dim(data)) > 2) {
     if (!is.null(lon_dim) & !is.null(lat_dim)) {
-      dimnames <- names(dim(var))
-      dim(var) <- dim(var)[which((dimnames == lon_dim | dimnames == lat_dim | dim(var) != 1))]
+      dimnames <- names(dim(data))
+      dim(data) <- dim(data)[which((dimnames == lon_dim | dimnames == lat_dim | dim(data) != 1))]
     } else {
-      if (all(dim(var) == 1)) {
-        dim(var) <- c(1, 1)
-      } else if (length(dim(var)[which(dim(var) > 1)]) == 2) {
-        var <- drop(var)
-      } else if (length(dim(var)[which(dim(var) > 1)]) == 1) {
-        dim(var) <- c(dim(var)[which(dim(var) > 1)], 1)
+      if (all(dim(data) == 1)) {
+        dim(data) <- c(1, 1)
+      } else if (length(dim(data)[which(dim(data) > 1)]) == 2) {
+        data <- drop(data)
+      } else if (length(dim(data)[which(dim(data) > 1)]) == 1) {
+        dim(data) <- c(dim(data)[which(dim(data) > 1)], 1)
       }
     }
   }
   
-  if (length(dim(var)) != 2) {
-    stop("Parameter 'var' must be a numeric array with two dimensions.")
+  if (length(dim(data)) != 2) {
+    stop("Parameter 'data' must be a numeric array with two dimensions.")
   }
   
-  if ((dim(var)[1] == length(lon) && dim(var)[2] == length(lat)) ||
-      (dim(var)[2] == length(lon) && dim(var)[1] == length(lat))) {
-    if (dim(var)[2] == length(lon) && dim(var)[1] == length(lat)) {
+  if ((dim(data)[1] == length(lon) && dim(data)[2] == length(lat)) ||
+      (dim(data)[2] == length(lon) && dim(data)[1] == length(lat))) {
+    if (dim(data)[2] == length(lon) && dim(data)[1] == length(lat)) {
       if (length(lon) == length(lat)) {
-        if (is.null(names(dim(var)))) {
-          warning("Parameter 'var' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the first and second dimensions.")
+        if (is.null(names(dim(data)))) {
+          warning("Parameter 'data' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the first and second dimensions.")
         } else {
-          if (names(dim(var)[1]) == lat_dim) {
+          if (names(dim(data)[1]) == lat_dim) {
             transpose <- TRUE
           }
         }
@@ -397,17 +406,17 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
       }   
     }
   } else {
-    stop("Parameters 'lon' and 'lat' must have as many elements as the number of cells along longitudes and latitudes in the input array 'var'.")
+    stop("Parameters 'lon' and 'lat' must have as many elements as the number of cells along longitudes and latitudes in the input array 'data'.")
   }
   
-  if (!is.null(names(dim(var)))) {
-    if (names(dim(var)[1]) == lon_dim) {
+  if (!is.null(names(dim(data)))) {
+    if (names(dim(data)[1]) == lon_dim) {
       if (transpose) {
-        stop("Coordinates dimensions of 'var' doesn't correspond to lat or lon.")
+        stop("Coordinates dimensions of 'data' doesn't correspond to lat or lon.")
       }
-    } else if (names(dim(var)[2]) == lon_dim) {
+    } else if (names(dim(data)[2]) == lon_dim) {
       if (!transpose) {
-        stop("Coordinates dimensions of 'var' doesn't correspond to lat or lon.")
+        stop("Coordinates dimensions of 'data' doesn't correspond to lat or lon.")
       }
     }
   }
@@ -416,13 +425,13 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
   # with dimensions c(lon, lat).
   
   if (transpose) {
-    var <- t(var)
+    data <- t(data)
   }
   
   transpose <- FALSE
   
-  names(dim(var)) <- c(lon_dim, lat_dim)
-  dims <- dim(var)
+  names(dim(data)) <- c(lon_dim, lat_dim)
+  dims <- dim(data)
   
   # Check varu and varv
   if (!is.null(varu) && !is.null(varv)) {
@@ -450,9 +459,9 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     } else {
       if (!is.null(names(dim(varu)))) {
         if (!(lon_dim %in% names(dim(varu)) && lat_dim %in% names(dim(varu)))) {
-          stop("Parameters 'varu' and 'varv' must have same dimension names as 'var'.")
-        } else if (dim(varu)[lon_dim] != dim(var)[lon_dim] || dim(varu)[lat_dim] != dim(var)[lat_dim]) {
-          stop("Parameters 'varu' and 'varv' must have same dimensions as 'var'.")
+          stop("Parameters 'varu' and 'varv' must have same dimension names as 'data'.")
+        } else if (dim(varu)[lon_dim] != dim(data)[lon_dim] || dim(varu)[lat_dim] != dim(data)[lat_dim]) {
+          stop("Parameters 'varu' and 'varv' must have same dimensions as 'data'.")
         }
       } else {
         warning("Parameters 'varu' and 'varv' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
@@ -503,9 +512,9 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     } else {
       if (!is.null(names(dim(contours)))) {
         if (!(lon_dim %in% names(dim(contours)) && lat_dim %in% names(dim(contours)))) {
-          stop("Parameters 'contours' must have same dimension names as 'var'.")
-        } else if (dim(contours)[lon_dim] != dim(var)[lon_dim] || dim(contours)[lat_dim] != dim(var)[lat_dim]) {
-          stop("Parameters 'contours' must have same dimensions as 'var'.")
+          stop("Parameters 'contours' must have same dimension names as 'data'.")
+        } else if (dim(contours)[lon_dim] != dim(data)[lon_dim] || dim(contours)[lat_dim] != dim(data)[lat_dim]) {
+          stop("Parameters 'contours' must have same dimensions as 'data'.")
         }
       } else {
         warning("Parameters 'contours' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
@@ -580,37 +589,37 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     stop("Parameter 'vertical' must be TRUE or FALSE.")
   }
   
-  tmp <- .create_var_limits(data = var, brks = brks, 
+  tmp <- .create_var_limits(data = data, brks = brks, 
                             bar_limits = bar_limits, drawleg = drawleg)
   var_limits <- tmp$var_limits
   drawleg <- tmp$drawleg
   
   # Check: brks, cols, subsampleg, bar_limits, color_fun, bar_extra_labels, draw_bar_ticks
-  #        draw_separators, triangle_ends_scale, label_scale, units, units_scale, 
+  #        draw_separators, triangle_ends_scale, bar_label_scale, units, units_scale, 
   #        bar_label_digits
   # Build: brks, cols, bar_limits, col_inf, col_sup
   colorbar <- ColorBarContinuous(brks, cols, vertical = vertical, subsampleg, bar_limits, 
                                  var_limits, triangle_ends, col_inf, col_sup, color_fun, FALSE, 
-                                 extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+                                 bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
                                  draw_separators = draw_separators, 
                                  triangle_ends_scale = triangle_ends_scale,
-                                 label_scale = bar_label_scale, title = units, 
-                                 title_scale = units_scale, tick_scale = bar_tick_scale,
-                                 extra_margin = bar_extra_margin, label_digits = bar_label_digits)
+                                 bar_label_scale = bar_label_scale, title = units, 
+                                 title_scale = units_scale, bar_tick_scale = bar_tick_scale,
+                                 bar_extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   brks <- colorbar$brks
   cols <- colorbar$cols
   col_inf <- colorbar$col_inf
   col_sup <- colorbar$col_sup
   bar_limits <- c(head(brks, 1), tail(brks, 1))
   
-  # Adjust 'var' values according to 'include_lower_boundary' and 'include_upper_boundary'.
+  # Adjust 'data' values according to 'include_lower_boundary' and 'include_upper_boundary'.
   # This adjustment ensures that, by default, values at the lower limit of the color bars ('brks[1]') are included. 
   # Refer to issue #15 in the esviz GitLab for more details.
   if (include_lower_boundary) {
-    var[var == head(brks, 1)] <- head(brks, 1) + head(diff(brks), 1)/10
+    data[data == head(brks, 1)] <- head(brks, 1) + head(diff(brks), 1)/10
   }
   if (!include_upper_boundary) {
-    var[var == tail(brks, 1)] <- tail(brks, 1) + tail(diff(brks), 1)/10
+    data[data == tail(brks, 1)] <- tail(brks, 1) + tail(diff(brks), 1)/10
   }  
   
   # Check colNA
@@ -739,7 +748,7 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     if (is.null(contours)) { 
       if (!square) {
         brks2 <- brks
-        contours <- var 
+        contours <- data 
       }
     } else {
       ll <- signif(min(contours, na.rm = TRUE), 2)
@@ -787,9 +796,9 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     } else {
       if (!is.null(names(dim(dots)))) {
         if (!(lon_dim %in% names(dim(dots)) && lat_dim %in% names(dim(dots)))) {
-          stop("Parameters 'dots' must have same dimension names as 'var'.")
-        } else if (dim(dots)[lon_dim] != dim(var)[lon_dim] || dim(dots)[lat_dim] != dim(var)[lat_dim]) {
-          stop("Parameters 'dots' must have same dimensions as 'var'.")
+          stop("Parameters 'dots' must have same dimension names as 'data'.")
+        } else if (dim(dots)[lon_dim] != dim(data)[lon_dim] || dim(dots)[lat_dim] != dim(data)[lat_dim]) {
+          stop("Parameters 'dots' must have same dimensions as 'data'.")
         }
       } else {
         warning("Parameters 'dots' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
@@ -813,7 +822,7 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
         }
       }
     } else {
-      stop("Parameter 'dots' must have same number of longitudes and latitudes as 'var'.")
+      stop("Parameter 'dots' must have same number of longitudes and latitudes as 'data'.")
     }
     
     if (transpose) {
@@ -848,14 +857,14 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
   if (!is.null(mask)) {
     mask <- drop(mask)
     if (!is.array(mask) || any(!names(dim(mask)) %in% c(lon_dim, lat_dim))) {
-      stop("Parameter 'mask' must have two dimensions named as the longitude and latitude dimensions in 'var'.")
+      stop("Parameter 'mask' must have two dimensions named as the longitude and latitude dimensions in 'data'.")
     } else {
-      if (!identical(names(dim(mask)), names(dim(var)))) {
-        mask <- aperm(mask, match(names(dim(mask)), names(dim(var))))
+      if (!identical(names(dim(mask)), names(dim(data)))) {
+        mask <- aperm(mask, match(names(dim(mask)), names(dim(data))))
       }
     }
-    if (!identical(dim(mask), dim(var))) {
-      stop("Parameter 'mask' must have the same dimensions as 'var'.")
+    if (!identical(dim(mask), dim(data))) {
+      stop("Parameter 'mask' must have the same dimensions as 'data'.")
     } else if (is.numeric(mask)) {
       if (all(mask %in% c(0, 1))) {
         mask <- array(as.logical(mask), dim = dim(mask))
@@ -882,7 +891,7 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
   if (!is.null(hatching_mask)) {
     hatching_mask <- drop(hatching_mask)
     if (!is.array(hatching_mask) || any(!names(dim(hatching_mask)) %in% c(lon_dim, lat_dim))) {
-      stop("Parameter 'hatching_mask' must have two dimensions named as the longitude and latitude dimensions in 'var'.")
+      stop("Parameter 'hatching_mask' must have two dimensions named as the longitude and latitude dimensions in 'data'.")
     }
   }
   
@@ -1218,18 +1227,18 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     # If lat and lon are both regular-spaced, "useRaster = TRUE" can avoid
     # artifact white lines on the figure. If not, useRaster has to be FALSE (default)
     tryCatch({
-      image(lonb$x, latb$x, var[lonb$ix, latb$ix], 
+      image(lonb$x, latb$x, data[lonb$ix, latb$ix], 
             col = c(col_inf_image, cols, col_sup_image), 
             breaks = c(-.Machine$double.xmax, brks, .Machine$double.xmax),
             axes = FALSE, xlab = "", ylab = "", add = TRUE, useRaster = TRUE)
     }, error = function(x) {
-      image(lonb$x, latb$x, var[lonb$ix, latb$ix], 
+      image(lonb$x, latb$x, data[lonb$ix, latb$ix], 
             col = c(col_inf_image, cols, col_sup_image), 
             breaks = c(-.Machine$double.xmax, brks, .Machine$double.xmax),
             axes = FALSE, xlab = "", ylab = "", add = TRUE)
     })
   } else {
-    .filled.contour(lonb$x, latb$x, var[lonb$ix, latb$ix], 
+    .filled.contour(lonb$x, latb$x, data[lonb$ix, latb$ix], 
                     levels = c(.Machine$double.xmin, brks, .Machine$double.xmax), 
                     col = c(col_inf_image, cols, col_sup_image))
   }
@@ -1252,13 +1261,13 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
   # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   #
   if (!is.null(dots)) {
-    data_avail <- !is.na(var)
+    data_avail <- !is.na(data)
     for (counter in 1:(dim(dots)[1])) {
       points <- which(dots[counter, , ] & data_avail, arr.ind = TRUE)
       points(lon[points[, 1]], lat[points[, 2]], 
              pch = dot_symbol[counter], 
-             cex = dot_size[counter] * 3 / sqrt(sqrt(length(var))),
-             lwd = dot_size[counter] * 3 / sqrt(sqrt(length(var))))
+             cex = dot_size[counter] * 3 / sqrt(sqrt(length(data))),
+             lwd = dot_size[counter] * 3 / sqrt(sqrt(length(data))))
     }
   }
   
@@ -1267,7 +1276,7 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
   # ~~~~~~~~~~~~~~~~~
   #
   if (!is.null(hatching_mask)) {
-    Hatching(hatching_mask = hatching_mask, lat = lat, lon = lon, data = var, 
+    Hatching(hatching_mask = hatching_mask, lat = lat, lon = lon, data = data, 
              hatching_density = hatching_density,
              hatching_angle = hatching_angle, 
              hatching_color = hatching_color, hatching_lwd = hatching_lwd, 
@@ -1486,11 +1495,11 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     }
     ColorBarContinuous(brks, cols, vertical = vertical, subsampleg, bar_limits,
                        var_limits, triangle_ends, col_inf = col_inf, col_sup = col_sup, 
-                       extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+                       bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
                        draw_separators = draw_separators, title = units, 
                        title_scale = units_scale, triangle_ends_scale = triangle_ends_scale, 
-                       label_scale = bar_label_scale, tick_scale = bar_tick_scale,
-                       extra_margin = bar_extra_margin, label_digits = bar_label_digits)
+                       bar_label_scale = bar_label_scale, bar_tick_scale = bar_tick_scale,
+                       bar_extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   }
   
   # If the graphic was saved to file, close the connection with the device
-- 
GitLab


From 9a5f2c612671f86a98f462d1d6d92cba3d7dc9db Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 25 Jun 2025 12:26:13 +0200
Subject: [PATCH 3/4] Update PlotCombinedMap.R to match esviz version

---
 modules/Visualization/R/tmp/PlotCombinedMap.R | 179 +++++++++++-------
 1 file changed, 107 insertions(+), 72 deletions(-)

diff --git a/modules/Visualization/R/tmp/PlotCombinedMap.R b/modules/Visualization/R/tmp/PlotCombinedMap.R
index e4d6d7f3..f80fdfcf 100644
--- a/modules/Visualization/R/tmp/PlotCombinedMap.R
+++ b/modules/Visualization/R/tmp/PlotCombinedMap.R
@@ -27,23 +27,33 @@
 #'@param map_dim Optional name for the dimension of 'maps' along which the 
 #'  multiple maps are arranged. Only applies when 'maps' is provided as a 
 #'  3-dimensional array. Takes the value 'map' by default.
-#'@param brks Colour levels to be sent to PlotEquiMap. This parameter is 
+#'@param brks Colour levels to be sent to VizEquiMap. This parameter is 
 #'  optional and adjusted automatically by the function.
-#'@param cols List of vectors of colours to be sent to PlotEquiMap for the 
+#'@param cols List of vectors of colours to be sent to VizEquiMap for the 
 #'  colour bar of each map. This parameter is optional and adjusted 
 #'  automatically by the function (up to 5 maps). The colours provided for each 
 #'  colour bar will be automatically interpolated to match the number of breaks. 
 #'  Each item in this list can be named, and the name will be used as title for 
 #'  the corresponding colour bar (equivalent to the parameter 'bar_titles').
+#'@param bar_limits A numeric vector of 2 indicating the range of color bar.
+#'  The default is NULL, and the function will decide the range automatically.
+#'@param triangle_ends A logical vector of two indicating if the lower and upper
+#'  triangles of the color bar should be plotted. The default is 
+#'  c(FALSE, FALSE).
+#'@param col_inf A character string of recognized color name or code indicating
+#'  the color of the lower triangle of the color bar. The default is NULL.
+#'@param col_sup A character string of recognized color name or code indicating
+#'  the color of the upper triangle of the color bar. The default is NULL.
 #'@param col_unknown_map Colour to use to paint the grid cells for which a map 
 #'  is not possible to be chosen according to 'map_select_fun' or for those 
 #'  values that go beyond 'display_range'. Takes the value 'white' by default.
 #'@param mask Optional numeric array with dimensions (latitude, longitude), with 
 #'  values in the range [0, 1], indicating the opacity of the mask over each 
 #'  grid point. Cells with a 0 will result in no mask, whereas cells with a 1 
-#'  will result in a totally opaque superimposed pixel coloured in 'col_mask'.
-#'@param col_mask Colour to be used for the superimposed mask (if specified in 
+#'  will result in a totally opaque superimposed pixel coloured in 'mask_color'.
+#'@param mask_color Colour to be used for the superimposed mask (if specified in 
 #'  'mask'). Takes the value 'grey' by default.
+#'@param col_mask Deprecated. Use 'mask_color' instead.
 #'@param dots Array of same dimensions as 'var' or with dimensions 
 #'  c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
 #'  plot. A value of TRUE at a grid cell will draw a dot/symbol on the 
@@ -52,20 +62,23 @@
 #'  layers via the parameter 'dot_symbol'.
 #'@param bar_titles Optional vector of character strings providing the titles to 
 #'  be shown on top of each of the colour bars.
-#'@param legend_scale Scale factor for the size of the colour bar labels. Takes 
+#'@param bar_label_scale Scale factor for the size of the colour bar labels. Takes 
 #'  1 by default.
 #'@param cex_bar_titles Scale factor for the sizes of the bar titles. Takes 1.5 
 #'  by default.
-#'@param plot_margin Numeric vector of length 4 for the margin sizes in the 
-#'  following order: bottom, left, top, and right. If not specified, use the 
-#'  default of par("mar"), c(5.1, 4.1, 4.1, 2.1). Used as 'margin_scale' in 
-#'  s2dv::PlotEquiMap.
+#'@param margin_scale Numeric vector of length 4 for the margin sizes in the 
+#'  following order: bottom, left, top, and right. If not specified (NULL), the 
+#'  default of par("mar"), c(5.1, 4.1, 4.1, 2.1), is used. Default is NULL.
+#'@param plot_margin Deprecated. Use 'margin_scale' instead.
+#'@param bar_extra_margin A numeric vector of 4 indicating the extra margins to
+#'  be added around the color bar, in the format c(y1, x1, y2, x2). The units 
+#'  are margin lines. The default values are c(2, 0, 2, 0).
 #'@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 File width, in the units specified in the parameter size_units 
+#'@param width File width, in the units specified in the parameter 'size_units' 
 #'  (inches by default). Takes 8 by default.
-#'@param height File height, in the units specified in the parameter size_units 
+#'@param height File height, in the units specified in the parameter 'size_units' 
 #'  (inches by default). Takes 5 by default.
 #'@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 
@@ -81,10 +94,10 @@
 #'@param return_leg A logical value indicating if the color bars information 
 #'  should be returned by the function. If TRUE, the function doesn't plot the
 #'  color bars but still creates the layout with color bar areas, and the 
-#'  arguments for GradientCatsColorBar() or ColorBar() will be returned. It is
-#'  convenient for users to adjust the color bars manually. The default is 
-#'  FALSE, the color bars will be plotted directly.
-#'@param ... Additional parameters to be passed on to \code{PlotEquiMap}.
+#'  arguments for GradientCatsColorBar() or ColorBarContinuous() will be 
+#'  returned. It is convenient for users to adjust the color bars manually. The 
+#'  default is FALSE, the color bars will be plotted directly.
+#'@param ... Additional parameters to be passed on to \code{VizEquiMap}.
 #' 
 #'@examples
 #'# Simple example
@@ -115,34 +128,34 @@
 #'                width = 14, height = 10) 
 #'}
 #'
-#'@seealso \code{PlotCombinedMap} and \code{PlotEquiMap}
-#' 
-#'@importFrom s2dv PlotEquiMap ColorBar
+#'@seealso \code{PlotCombinedMap} and \code{VizEquiMap}
+#'
+#'@import utils 
 #'@importFrom maps map 
 #'@importFrom graphics box image layout mtext par plot.new
 #'@importFrom grDevices adjustcolor bmp colorRampPalette dev.cur dev.new dev.off 
 #'  hcl jpeg pdf png postscript svg tiff
 #'@export
 PlotCombinedMap <- function(maps, lon, lat, 
-                            map_select_fun, display_range, 
-                            map_dim = 'map',
-                            brks = NULL, cols = NULL,  
-                            bar_limits = NULL, triangle_ends = c(F, F), col_inf = NULL, col_sup = NULL,
-                            col_unknown_map = 'white',
-                            mask = NULL, col_mask = 'grey',
-                            dots = NULL,
-                            bar_titles = NULL, legend_scale = 1,
-                            cex_bar_titles = 1.5,
-                            plot_margin = NULL, bar_extra_margin = c(2, 0, 2, 0),
-                            fileout = NULL, width = 8, height = 5, 
-                            size_units = 'in', res = 100, drawleg = T, return_leg = FALSE,
-                            ...) {
+                           map_select_fun, display_range, 
+                           map_dim = 'map',
+                           brks = NULL, cols = NULL,  
+                           bar_limits = NULL, triangle_ends = c(FALSE, FALSE), 
+                           col_inf = NULL, col_sup = NULL,
+                           col_unknown_map = 'white',
+                           mask = NULL, mask_color = 'grey', col_mask = NULL,
+                           dots = NULL,
+                           bar_titles = NULL, bar_label_scale = 1,
+                           cex_bar_titles = 1.5, margin_scale = NULL,
+                           plot_margin = NULL, bar_extra_margin = c(2, 0, 2, 0),
+                           fileout = NULL, width = 8, height = 5, 
+                           size_units = 'in', res = 100, drawleg = T,
+                           return_leg = FALSE, ...) {
   args <- list(...)
-
+  
   # If there is any filenames to store the graphics, process them
   # to select the right device 
   if (!is.null(fileout)) {
-    .SelectDevice <- utils::getFromNamespace(".SelectDevice", "s2dv")
     deviceInfo <- .SelectDevice(fileout = fileout, width = width, height = height, 
                                 units = size_units, res = res)
     saveToFile <- deviceInfo$fun
@@ -270,12 +283,12 @@ PlotCombinedMap <- function(maps, lon, lat,
                                    subsampleg = NULL, bar_limits = bar_limits,
                                    var_limits = var_limits_maps,
                                    triangle_ends = triangle_ends, col_inf = col_inf, col_sup = col_sup, plot = FALSE, draw_separators = TRUE,
-                                   bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = legend_scale * 1.5,
+                                   bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = bar_label_scale * 1.5,
                                    extra_margin = bar_extra_margin)
   
-  # Check legend_scale
-  if (!is.numeric(legend_scale)) {
-    stop("Parameter 'legend_scale' must be numeric.")
+  # Check bar_label_scale
+  if (!is.numeric(bar_label_scale)) {
+    stop("Parameter 'bar_label_scale' must be numeric.")
   }
   
   # Check col_unknown_map
@@ -283,9 +296,13 @@ PlotCombinedMap <- function(maps, lon, lat,
     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_color
+  if (missing(mask_color) && !missing(col_mask)) {
+    warning("The parameter 'col_mask' is deprecated. Use 'mask_color' instead.")
+    mask_color <- col_mask
+  }
+  if (!is.character(mask_color)) {
+    stop("Parameter 'mask_color' must be a character string.")
   }
   
   # Check mask
@@ -301,6 +318,7 @@ PlotCombinedMap <- function(maps, lon, lat,
       stop("Parameter 'mask' must have dimensions c(lat, lon).")
     }
   }
+  
   # Check dots
   if (!is.null(dots)) {
     if (length(dim(dots)) != 2) {
@@ -311,12 +329,27 @@ PlotCombinedMap <- function(maps, lon, lat,
       stop("Parameter 'mask' must have dimensions c(lat, lon).")
     }
   }
- 
+  
+  # Check margin_scale
+  if (missing(margin_scale) && !missing(plot_margin)) {
+    warning("The parameter 'plot_margin' is deprecated. Use 'margin_scale' instead.")
+    margin_scale <- plot_margin
+  }
+  if (!is.null(margin_scale)) {
+    if (!is.numeric(margin_scale) || length(margin_scale) != 4) {
+      stop("Parameter 'margin_scale' must be a numeric vector of length 4: c(bottom, left, top, right).")
+    }
+  }
+  
   #----------------------
   # Identify the most likely map
   #----------------------
+  #TODO: Consider col_inf
+  if (!is.null(colorbar$col_inf[[1]])) {
+    warning("Lower triangle is not supported now. Please contact maintainer if you have this need.")
+  }
   if (!is.null(colorbar$col_sup[[1]])) {
-
+    
     brks_norm <- vector('list', length = nmap)
     range_width <- vector('list', length = nmap)
     slightly_tune_val <- vector('list', length = nmap)
@@ -339,7 +372,7 @@ PlotCombinedMap <- function(maps, lon, lat,
               res <- res + 1 - slightly_tune_val[[res_ind]]
             } else {
               res <- res + ((map_select_fun(x) - colorbar$brks[[res_ind]][1]) /
-                range_width[[res_ind]] * ((length(brks_norm[[res_ind]]) - 2) / (length(brks_norm[[res_ind]]) - 1)))
+                              range_width[[res_ind]] * ((length(brks_norm[[res_ind]]) - 2) / (length(brks_norm[[res_ind]]) - 1)))
               if (map_select_fun(x) == colorbar$brks[[res_ind]][1]) {
                 res <- res + slightly_tune_val[[res_ind]]
               }
@@ -351,15 +384,16 @@ PlotCombinedMap <- function(maps, lon, lat,
       }
       res
     })
-
+    
   } else {
-
+    
     brks_norm <- vector('list', length = nmap)
-    range_width <- display_range[2] - display_range[1] #vector('list', length = nmap)
+    range_width <- vector('list', length = nmap)
     slightly_tune_val <- vector('list', length = nmap)
     for (ii in 1:nmap) {
       brks_norm[[ii]] <- seq(0, 1, length.out = length(colorbar$brks[[ii]]))
       slightly_tune_val[[ii]] <- brks_norm[[ii]][2] / (length(brks_norm[[ii]]) * 2)
+      range_width[[ii]] <- diff(range(colorbar$brks[[ii]]))
     }
     ml_map <- apply(maps, c(lat_dim, lon_dim), function(x) {
       if (any(is.na(x))) {
@@ -367,14 +401,15 @@ PlotCombinedMap <- function(maps, lon, lat,
       } else {
         res <- which(x == map_select_fun(x))
         if (length(res) > 0) {
-          res <- res[1]
+          res <- res_ind <- res[1]
           if (map_select_fun(x) < display_range[1] ||
-            map_select_fun(x) > display_range[2]) {
+              map_select_fun(x) > display_range[2]) {
             res <- -0.5
           } else {
-            res <- res + (map_select_fun(x) - display_range[1]) / range_width
-            if (map_select_fun(x) == display_range[1]) {
-              res <- res + slightly_tune_val
+            res <- res + ((map_select_fun(x) - colorbar$brks[[res_ind]][1]) /
+                            range_width[[res_ind]]) 
+            if (map_select_fun(x) == colorbar$brks[[res_ind]][1]) {
+              res <- res + slightly_tune_val[[res_ind]]
             }
           }
         } else {
@@ -384,7 +419,7 @@ PlotCombinedMap <- function(maps, lon, lat,
       res
     })
   }
-
+  
   nlat <- length(lat)
   nlon <- length(lon)
   
@@ -413,18 +448,18 @@ PlotCombinedMap <- function(maps, lon, lat,
     dev.new(units = size_units, res = res, width = width, height = height)
   }
   #NOTE: I think plot.new() is not necessary in any case.
-#  plot.new()
+  #  plot.new()
   #TODO: Don't hardcoded. Let users decide.
   par(font.main = 1)
   # If colorbars need to be plotted, re-define layout.
   if (drawleg) {
     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
+  # Set colors and breaks and then VizEquiMap
   #----------------------
- if (!is.null(colorbar$col_sup[[1]])) {
+  if (!is.null(colorbar$col_sup[[1]])) {
     tcols <- c(col_unknown_map, colorbar$cols[[1]], colorbar$col_sup[[1]])
     tbrks <- c(-1, brks_norm[[1]] + rep(1, each = length(brks_norm[[1]])))
     for (k in 2:nmap) {
@@ -439,14 +474,14 @@ PlotCombinedMap <- function(maps, lon, lat,
       tbrks <- c(tbrks, brks_norm[[k]] + rep(k, each = length(brks_norm[[k]])))
     }
   }
-
-  if (is.null(plot_margin)) {
-    plot_margin <- c(5, 4, 4, 2) + 0.1  # default of par()$mar
+  
+  if (is.null(margin_scale)) {
+    margin_scale <- c(5, 4, 4, 2) + 0.1  # default of par()$mar
   }
-
-  PlotEquiMap(var = ml_map, lon = lon, lat = lat, 
-              brks = tbrks, cols = tcols, drawleg = FALSE, 
-              filled.continents = FALSE, dots = dots, margin_scale = plot_margin, ...)
+  
+  VizEquiMap(var = ml_map, lon = lon, lat = lat, 
+             brks = tbrks, cols = tcols, drawleg = FALSE, 
+             filled.continents = FALSE, dots = dots, margin_scale = margin_scale, ...)
   
   #----------------------
   # Add overplot on top
@@ -460,9 +495,9 @@ PlotCombinedMap <- function(maps, lon, lat,
       lon[(wher + 1):dims_mask[2]] <- lon[(wher + 1):dims_mask[2]] - 360
     }
     lonb <- sort(lon, index.return = TRUE)
-
+    
     cols_mask <- sapply(seq(from = 0, to = 1, length.out = 10), 
-                        function(x) adjustcolor(col_mask, alpha.f = x))
+                        function(x) adjustcolor(mask_color, alpha.f = x))
     image(lonb$x, latb$x, t(mask)[lonb$ix, latb$ix], 
           axes = FALSE, col = cols_mask, 
           breaks = seq(from = 0, to = 1, by = 0.1), 
@@ -490,7 +525,7 @@ PlotCombinedMap <- function(maps, lon, lat,
     old_mar[3] <- old_mar[3] - (2 * size_title + 1)
     par(mar = old_mar)
   }
-
+  
   if (drawleg & !return_leg) {
     GradientCatsColorBar(nmap = dim(maps)[map_dim],
                          brks = colorbar$brks, cols = colorbar$cols, vertical = FALSE,
@@ -498,15 +533,15 @@ PlotCombinedMap <- function(maps, lon, lat,
                          var_limits = var_limits_maps,
                          triangle_ends = triangle_ends, col_inf = colorbar$col_inf, col_sup = colorbar$col_sup,
                          plot = TRUE, draw_separators = TRUE,
-                         bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = legend_scale * 1.5,
+                         bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = bar_label_scale * 1.5,
                          extra_margin = bar_extra_margin)
   }
-
+  
   if (!return_leg) {
     # If the graphic was saved to file, close the connection with the device
     if (!is.null(fileout)) dev.off()
   }
-
+  
   if (return_leg) {
     tmp <- list(nmap = dim(maps)[map_dim],
                 brks = colorbar$brks, cols = colorbar$cols, vertical = FALSE,
@@ -514,12 +549,12 @@ PlotCombinedMap <- function(maps, lon, lat,
                 var_limits = var_limits_maps,
                 triangle_ends = triangle_ends, col_inf = colorbar$col_inf, col_sup = colorbar$col_sup,
                 plot = TRUE, draw_separators = TRUE,
-                bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = legend_scale * 1.5,
+                bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = bar_label_scale * 1.5,
                 extra_margin = bar_extra_margin)
+    warning("The device is not off yet. Use dev.off() after plotting the color bars.")
     return(tmp)
     #NOTE: The device is not off! Can keep plotting the color bars.
   }
-
+  
 }
 
-
-- 
GitLab


From 82c46af7515a84bd9a29e098b8467a12b721f935 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 25 Jun 2025 12:26:41 +0200
Subject: [PATCH 4/4] Update PlotRobinson.R to match esviz version

---
 modules/Visualization/R/tmp/PlotRobinson.R | 402 +++++++++++----------
 1 file changed, 221 insertions(+), 181 deletions(-)

diff --git a/modules/Visualization/R/tmp/PlotRobinson.R b/modules/Visualization/R/tmp/PlotRobinson.R
index 67ca034d..adff5674 100644
--- a/modules/Visualization/R/tmp/PlotRobinson.R
+++ b/modules/Visualization/R/tmp/PlotRobinson.R
@@ -4,7 +4,7 @@
 #'plot the map. The target projection must be a valid CRS string, preferrably be 
 #'EPSG or ESRI code; check \link[sf]{st_crs} for more explanation. This function
 #'is mainly tested for Robinson projection (ESRI:54030), but it can work with 
-#'other projection types in theory.\n
+#'other projection types in theory.\cr
 #'The map can be plotted by points or polygon. A legend can be plotted as either
 #'a color bar or a discrete ggplot legend. Dots can be drawn on top of the data,
 #'which can be used for significance test. A mask can be added to not plot the 
@@ -21,17 +21,19 @@
 #'  of ascending or descending order.
 #'@param lon_dim A character string indicating the longitude dimension name in
 #'  'data'. If it is NULL, the function tries to find the name in 
-#'  \code{s2dv:::.KnownLonNames}. The default value is NULL.
+#'  \code{esviz:::.KnownLonNames}. The default value is NULL.
 #'@param lat_dim A character string indicating the latitude dimension name in
 #'  'data'. If it is NULL, the function tries to find the name in 
-#'  \code{s2dv:::.KnownLatNames}. The default value is NULL.
+#'  \code{esviz:::.KnownLatNames}. The default value is NULL.
 #'@param target_proj A character string indicating the target projection. It 
-#'  should be a valid crs string. The default projection is Robinson 
-#'  (ESRI:54030). Note that the character string may work differently depending
-#'  on PROJ and GDAL module version.
-#'@param legend A character string indicating the legend style. It can be 's2dv'
-#'  (color bar by \code{ColorBar()}), 'ggplot2' (discrete legend by ggplot2), or
-#'  NULL (no legend),
+#'  should be a valid crs string. The default projection is Robinson: 
+#'  "ESRI:54030". Note that the character string may work differently depending
+#'  on PROJ and GDAL module version. If package version 'sf' is lower than 
+#'  "1.0.10" and an error appears regarding the target crs, you can try with 
+#'  numeric crs (e.g. target_proj = 54030).
+#'@param drawleg A character string indicating the legend style. It can be 
+#'  'bar' (color bar by \code{ColorBarContinuous()}), 'ggplot2' (discrete legend 
+#'  by ggplot2), or FALSE (no legend). The default value is 'bar'.
 #'@param style A character string indicating the plotting style. It can be 
 #'  'point' or 'polygon'. The default value is 'point'. Note that 'polygon' may
 #'  be time- and memory-consuming for global or high-resolution data.
@@ -46,23 +48,24 @@
 #'  define n breaks that define n - 1 intervals to classify each of the values 
 #'  in 'data'. The corresponding grid cell of a given value in 'data' will be 
 #'  colored 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.
+#'  sent to \code{ColorBarContinuous()} to generate the breaks and colours. 
+#'  Additional colors 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 ?ColorBarContinuous for
+#'  a full explanation.
 #'@param col_inf,col_sup,colNA Colour identifiers to color the values that 
 #'  excess the extremes of the color bar and to color NAs, respectively. 'colNA'
 #'  takes attr(cols, 'na_color') if available by default, where cols is the 
 #'  parameter 'cols' if provided or the vector of colors returned by 
 #'  'color_fun'. 'col_inf' and 'col_sup' will take the value of 'colNA' if not 
-#'  specified. See ?ColorBar for a full explanation.
+#'  specified. See ?ColorBarContinuous for a full explanation.
 #'@param color_fun,bar_extra_margin Set of 
 #'  parameters to control the visual aspect of the drawn colour bar 
-#'  (1/3). See ?ColorBar for a full explanation.
+#'  (1/3). See ?ColorBarContinuous for a full explanation.
 #'@param vertical A logical value indicating the direction of colorbar if 
-#' parameter 'legend' is 's2dv'. The default value is TRUE.
+#' parameter 'drawleg' is 'bar'. The default value is TRUE.
 #'@param toptitle A character string of the top title of the figure, scalable 
-#'  with parameter 'title_size'.
+#'  with parameter 'title_scale'.
 #'@param caption A character string of the caption located at left-bottom of the
 #'  plot.
 #'@param units A character string of the data units, which is the title of the 
@@ -72,11 +75,16 @@
 #'  cannot exceed 180 degrees.
 #'@param point_size A number of the size of the data points if "style = 'point'".
 #'  The default is 'auto' and the function tries to find the appropriate size.
-#'@param title_size A number of the size of the top title. The default is 16.
-#'@param dots_size A number of the size of the dots. The default is 0.5.
-#'@param dots_shape A number indicating the dot shape recognized by parameter 
+#'@param title_scale A number of the size of the top title. The default is 16.
+#'@param title_size Deprecated. Use 'title_scale' instead.
+#'@param dot_size A number of the size of the dots. The default is 0.5.
+#'@param dots_size Deprecated. Use 'dot_size' instead.
+#'@param dot_symbol A number indicating the dot shape recognized by parameter 
 #'  'shape' in \code{geom_point()}.
-#'@param coastlines_width A number indicating the width of the coastlines.
+#'@param dots_shape Deprecated. Use 'dot_symbol' instead.
+#'@param coast_width A number indicating the width of the coastlines. Default is
+#'  0.3.
+#'@param coastlines_width Deprecated. Use 'coast_width' instead.
 #'@param fileout A character string of the path to save the plot. If not 
 #'  specified (default), a graphic device will pop up. The extension should be  
 #'  accepted by \code{ggsave()}.
@@ -94,37 +102,43 @@
 #'@return A map plot with speficied projection, either in pop-up window or a 
 #'  saved file.
 #'
-#'@examples 
-#'data <- array(rep(seq(-10, 10, length.out = 181), 360) + rnorm(360), 
+#'@examples
+#'data <- array(rep(seq(-10, 10, length.out = 181), 360) + rnorm(360),
 #'              dim = c(lat = 181, lon = 360))
 #'dots <- data
 #'dots[which(dots < 4 & dots > -4)] <- 0
 #'dots[which(dots != 0)] <- 1
-#'PlotRobinson(data, lon = 0:359, lat = -90:90, dots = dots, 
-#'             brks = seq(-10, 10, length.out = 11), 
-#'             toptitle = 'synthetic example', vertical = F,
-#'             caption = 'Robinson Global\ns2dv::PlotRobinson example',
-#'             bar_extra_margin = c(0, 1, 0, 1), width = 8, height = 6)
-#'PlotRobinson(data, lon = 0:359, lat = -90:90, mask = dots, legend = 'ggplot2',
-#'             target_proj = "+proj=moll", brks = seq(-10, 10, length.out = 11),
-#'             color_fun = clim.palette("purpleorange"), colNA = 'green',
-#'             toptitle = 'synthetic example', 
-#'             caption = 'Mollweide Global\ns2dv::PlotRobinson example',
-#'             width = 8, height = 6)
-#'
-#'@import sf ggplot2 rnaturalearth cowplot
+#'  \dontrun{
+#'PlotRobinson(data, lon = 0:359, lat = -90:90, dots = dots,
+#'            brks = seq(-10, 10, length.out = 11),
+#'            toptitle = 'synthetic example', vertical = FALSE,
+#'            caption = 'Robinson Projection',
+#'            bar_extra_margin = c(0, 1, 0, 1), width = 8, height = 6)
+#'PlotRobinson(data, lon = 0:359, lat = -90:90, mask = dots, drawleg = 'ggplot2',
+#'            target_proj = "+proj=moll", brks = seq(-10, 10, length.out = 11),
+#'            color_fun = ClimPalette("purpleorange"), colNA = 'green',
+#'            toptitle = 'synthetic example', caption = 'Mollweide Projection',
+#'            width = 8, height = 6)
+#'  }
+#'@import sf ggplot2 rnaturalearth cowplot utils
+#'@importFrom dplyr mutate group_by summarise
+#'@importFrom ClimProjDiags Subset
+#'@importFrom rlang .data
 #'@export
-PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL, 
-                         target_proj = 54030, legend = 's2dv', style = 'point', 
-                         dots = NULL, mask = NULL, brks = NULL, cols = NULL, bar_limits = NULL,
-                         triangle_ends = NULL, col_inf = NULL, col_sup = NULL, colNA = NULL, 
-                         color_fun = clim.palette(), bar_extra_margin = c(3.5, 0, 3.5, 0), vertical = TRUE,
-                         toptitle = NULL, caption = NULL, units = NULL, crop_coastlines = NULL,
-                         point_size = "auto", title_size = 10, dots_size = 0.2,
-                         dots_shape = 47, coastlines_width = 0.3,
-                         fileout = NULL, width = 8, height = 5, size_units = "in", 
-                         res = 300) {
-
+PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
+                        target_proj = NULL, drawleg = 'bar', style = 'point', 
+                        dots = NULL, mask = NULL, brks = NULL, cols = NULL,
+                        bar_limits = NULL, triangle_ends = NULL, col_inf = NULL,
+                        col_sup = NULL, colNA = NULL, color_fun = ClimPalette(),
+                        bar_extra_margin = rep(0, 4), vertical = TRUE,
+                        toptitle = NULL, caption = NULL, units = NULL,
+                        crop_coastlines = NULL, point_size = "auto",
+                        title_scale = 16, title_size = NULL, dot_size = 0.5,
+                        dots_size = NULL, dot_symbol = 47, dots_shape = NULL,
+                        coast_width = 0.3, coastlines_width = NULL,
+                        fileout = NULL, width = 8, height = 4,
+                        size_units = "in", res = 300) {
+  
   # Sanity check
   # data
   data <- drop(data)
@@ -140,7 +154,7 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     }
   }
   if (is.unsorted(lon)) {
-    .warning("Parameter 'lon' should be sorted to guarantee the correct result.")
+    warning("Parameter 'lon' should be sorted to guarantee the correct result.")
   }
   # lat, lat_dim
   if (is.null(lat_dim)) {
@@ -158,7 +172,10 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
   if (length(lat) != dims[lat_dim]) {
     stop("Length of parameter 'lat' should match latitude dimension in 'data'.")
   }
-  data <- s2dv::Reorder(data, c(lon_dim, lat_dim))
+  
+  # Reorder data
+  data <- aperm(data, match(names(dim(data)), c(lon_dim, lat_dim)))
+  
   # Make lat always from 90 to -90
   sort_lat <- FALSE
   if (!is.unsorted(lat)) {
@@ -166,25 +183,28 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     data <- ClimProjDiags::Subset(data, along = lat_dim, indices = seq(length(lat), 1, -1))
     sort_lat <- TRUE
   }
-
+  
   # original_proj: it can only be regular grid now
   original_proj <- st_crs(4326)
-  # tartget_proj
+  # target_proj
   if (is.null(target_proj)) {
-    stop("Parameter 'target_proj' cannot be NULL.")
-  } else {
-    target_proj_tmp <- st_crs(target_proj)
-    if (is.na(target_proj_tmp)) {
-      .warning(paste0("Try ESRI code: ESRI:", target_proj))
-      target_proj <- st_crs(paste0("ESRI:", target_proj))
+    if (packageVersion("sf") < "1.0.10") {
+      target_proj <- 54030
     } else {
-      target_proj <- target_proj_tmp
+      target_proj <- "ESRI:54030"
     }
   }
-
-  # legend
-  if (!is.null(legend) && (!legend %in% c('s2dv', 'ggplot2'))) {
-    stop("Parameter 'legend' must be NULL, ggplot2 or s2dv.")
+  target_proj_tmp <- st_crs(target_proj)
+  if (is.na(target_proj_tmp)) {
+    warning(paste0("Try ESRI code: ESRI:", target_proj))
+    target_proj <- st_crs(paste0("ESRI:", target_proj))
+  } else {
+    target_proj <- target_proj_tmp
+  }
+  
+  # drawleg
+  if (!drawleg %in% c('bar', 'ggplot2', FALSE)) {
+    stop("Parameter 'drawleg' must be FALSE, 'ggplot2' or 'bar'.")
   }
   # style
   if (!style %in% c('point', 'polygon') || length(style) != 1) {
@@ -195,17 +215,17 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     if ((abs(diff(range(lon))) > 350 & abs(diff(range(lat))) > 175) |
         (prod(dim(data)) >= (180 * 360))) {
       if (!isTRUE(utils::askYesNo("The region seems to be global and style 'polygon' is chosen. It may be time- and memory-consuming to plot the map. Are you sure that you want to continue?"))) {
-       return(invisible())
+        return(invisible())
       }
     }
   }
   # dots
   if (!is.null(dots)) {
     dots <- drop(dots)
-    if (any(!names(dim(dots)) %in% c(lon_dim, lat_dim))) {
+    if (!is.array(dots) || any(!names(dim(dots)) %in% c(lon_dim, lat_dim))) {
       stop("Parameter 'dots' must have two dimensions named as longitude and latitude dimensions in 'data'.")
     } else {
-      dots <- Reorder(dots, c(lon_dim, lat_dim))
+      dots <- aperm(dots, match(names(dim(dots)), c(lon_dim, lat_dim)))
     }
     if (!identical(dim(dots), dim(data))) {
       stop("Parameter 'dots' must have the same dimensions as 'data'.")
@@ -226,10 +246,10 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
   # mask
   if (!is.null(mask)) {
     mask <- drop(mask)
-    if (any(!names(dim(mask)) %in% c(lon_dim, lat_dim))) {
+    if (!is.array(mask) || any(!names(dim(mask)) %in% c(lon_dim, lat_dim))) {
       stop("Parameter 'mask' must have two dimensions named as longitude and latitude dimensions in 'data'.")
     } else {
-      mask <- Reorder(mask, c(lon_dim, lat_dim))
+      mask <- aperm(mask, match(names(dim(mask)), c(lon_dim, lat_dim)))
     }
     if (!identical(dim(mask), dim(data))) {
       stop("Parameter 'mask' must have the same dimensions as 'data'.")
@@ -249,38 +269,31 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
       stop("Parameter 'mask' must be a logical or numerical array.")
     }
   }
-
+  # Check title_scale
+  if (missing(title_scale) && !missing(title_size)) {
+    warning("The parameter 'title_size' is deprecated. Use 'title_scale' instead.")
+    title_scale <- title_size
+  }
+  if (!is.numeric(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'title_scale' must be a single numerical value.")
+  }
+  
+  tmp <- .create_var_limits(data = data, brks = brks, 
+                            bar_limits = bar_limits, drawleg = drawleg)
+  var_limits <- tmp$var_limits
+  drawleg <- tmp$drawleg
+  
   # Color bar
   ## Check: brks, cols, bar_limits, color_fun, bar_extra_margin, units 
   ## Build: brks, cols, bar_limits, col_inf, col_sup
-  if (!all(is.na(data))) {
-    var_limits <- c(min(data[!is.infinite(data)], na.rm = TRUE),
-                    max(data[!is.infinite(data)], na.rm = TRUE))
-  } else {
-    warning("All the data are NAs. The map will be filled with colNA.")
-    if (!is.null(brks) && length(brks) > 1) {
-      #NOTE: var_limits be like this to avoid warnings from ColorBar
-      var_limits <- c(min(brks, na.rm = TRUE) + diff(brks)[1],
-                      max(brks, na.rm = TRUE))
-    } else if (!is.null(bar_limits)) {
-      var_limits <- c(bar_limits[1] + 0.01, bar_limits[2])
-    } else {
-      var_limits <- c(-0.5, 0.5) # random range since colorbar is not going to be plotted
-      if (!is.null(legend)) {
-        legend <- NULL
-        warning("All data are NAs. Color bar won't be drawn. If you want to have ",
-                 "color bar still, define parameter 'brks' or 'bar_limits'.")
-      }
-    }
-  }
-  colorbar <- ColorBar(brks = brks, cols = cols, vertical = vertical, subsampleg = NULL,
-                       bar_limits = bar_limits, var_limits = var_limits, triangle_ends = triangle_ends, 
-                       col_inf = col_inf, col_sup = col_sup, color_fun = color_fun, 
-                       plot = FALSE, draw_ticks = TRUE, draw_separators = FALSE,
-                       triangle_ends_scale = 1, extra_labels = NULL,
-                       title = units, title_scale = 1, # units_scale
-                       label_scale = 1, tick_scale = 1, #bar_tick_scale
-                       extra_margin = bar_extra_margin, label_digits = 4)
+  colorbar <- ColorBarContinuous(brks = brks, cols = cols, vertical = vertical, subsampleg = NULL,
+                                 bar_limits = bar_limits, var_limits = var_limits, triangle_ends = triangle_ends, 
+                                 col_inf = col_inf, col_sup = col_sup, color_fun = color_fun, 
+                                 plot = FALSE, draw_bar_ticks = TRUE, draw_separators = FALSE,
+                                 triangle_ends_scale = 1, bar_extra_labels = NULL,
+                                 title = units, title_scale = 1, # units_scale
+                                 bar_label_scale = 1, bar_tick_scale = 1,
+                                 bar_extra_margin = bar_extra_margin, bar_label_digits = 4)
   brks <- colorbar$brks
   cols <- colorbar$cols
   col_inf <- colorbar$col_inf
@@ -316,26 +329,52 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
       stop("Parameter 'crop_coastlines' needs to have names 'latmax', 'latmin', 'lonmax', 'lonmin'.")
     }
   }
-
+  
   # point_size
   if (point_size == 'auto') {
     # 360x181 with default setting, 0.05
     point_size <- round(0.05 * (360 * 181) / (length(lon) * length(lat)), 2)
   } else if (!is.numeric(point_size)) {
-    stop("Parameter 'point_size' must be a number.")
-  }
-  #
-
-#=================================================================
-
-  # Adapt s2dv ColorBar parameters to ggplot plot
-  # If legend is NULL, still tune with s2dv legend way
-  if (is.null(legend) || legend == 's2dv') {
+    stop("Parameter 'point_size' must be a numerical value.")
+  }
+  
+  # dot_symbol
+  if (missing(dot_symbol) && !missing(dots_shape)) {
+    warning("The parameter 'dots_shape' is deprecated. Use 'dot_symbol' instead.")
+    dot_symbol <- dots_shape
+  }
+  if (!is.numeric(dot_symbol)) {
+    stop("Parameter 'dot_symbol' must be a numerical value.")
+  }
+  
+  # dot_size
+  if (missing(dot_size) && !missing(dots_size)) {
+    warning("The parameter 'dots_size' is deprecated. Use 'dot_size' instead.")
+    dot_size <- dots_size
+  }
+  if (!is.numeric(dot_size)) {
+    stop("Parameter 'dot_size' must be a numerical value.")
+  }
+  
+  # coast_width
+  if (missing(coast_width) && !missing(coastlines_width)) {
+    warning("The parameter 'coastlines_width' is deprecated. Use 'coast_width' instead.")
+    coast_width <- coastlines_width
+  }
+  if (!is.numeric(coast_width)) {
+    stop("Parameter 'coast_width' must be a numerical value.")
+  }
+  
+  #=================================================================
+  
+  # Adapt ColorBarContinuous parameters to ggplot plot
+  # If drawleg is FALSE, still tune with bar legend way
+  if (isFALSE(drawleg) || drawleg == 'bar') {
     # the colorbar triangle color. If it is NULL (no triangle plotted), use colNA
     col_inf_image <- ifelse(is.null(col_inf), colNA, col_inf)
     col_sup_image <- ifelse(is.null(col_sup), colNA, col_sup)
     cols_ggplot <- c(col_inf_image, cols, col_sup_image)
-
+    
     # Add triangles to brks
     brks_ggplot <- brks
     if (var_limits[2] > tail(brks, 1)) {
@@ -348,19 +387,20 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     } else {
       brks_ggplot <- c(brks[1] - diff(brks[1:2]), brks_ggplot)
     }
-
+    
   } else {  # ggplot2 legend
     brks_ggplot <- brks
     cols_ggplot <- cols
   }
-
+  
   # Build data dataframe
   lonlat_df <- data.frame(lon = rep(as.vector(lon), length(lat)),
                           lat = sort(rep(as.vector(lat), length(lon)), decreasing = TRUE))
   data_df <- lonlat_df %>%
     dplyr::mutate(dat = as.vector(data))
-
+  
   lonlat_df_ori <- NULL
+  
   # Remove the points where mask = FALSE
   if (!is.null(mask)) {
     # Save original lonlat_df to plot with expected region
@@ -368,7 +408,7 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     lonlat_df_ori <- st_transform(lonlat_df_ori, crs = target_proj)
     lonlat_df_ori <- as.data.frame(st_coordinates(lonlat_df_ori))
     names(lonlat_df_ori) <- c('long', 'lat')
-
+    
     if (sort_lat) {
       mask <- ClimProjDiags::Subset(mask, along = lat_dim, indices = seq(length(lat), 1, -1))
     }
@@ -378,14 +418,14 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     data_df <- data_df[mask_df$mask == TRUE, ]
     lonlat_df <- data_df[, 1:2]
   }
-
+  
   #NOTE: if target_proj = "ESRI:54030", Nord3v2 has different behavior from hub and ws!!
   data_df <- st_as_sf(data_df, coords = c("lon", "lat"), crs = original_proj)
   data_df <- st_transform(data_df, crs = target_proj)
   data_df <- data_df %>%
     dplyr::mutate(long = st_coordinates(data_df)[, 1],
                   lat = st_coordinates(data_df)[, 2])
-
+  
   # Re-project dots
   if (!is.null(dots)) {
     if (sort_lat) {
@@ -394,29 +434,29 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     dots_df <- data.frame(lon = rep(as.vector(lon), length(lat)),
                           lat = sort(rep(as.vector(lat), length(lon)), decreasing = TRUE),
                           dot = as.vector(dots))
-
+    
     dots_df <- st_as_sf(dots_df, coords = c("lon", "lat"), crs = original_proj)
     dots_df <- st_transform(dots_df, crs = target_proj)
     dots_df <- dots_df %>%
       dplyr::mutate(long = st_coordinates(dots_df)[, 1],
                     lat = st_coordinates(dots_df)[, 2])
-    dots_df <- subset(dots_df, dot == FALSE)
+    dots_df <- dplyr::filter(dots_df, .data$dot == FALSE)
   }
-
+  
   # coastlines
   coastlines <- rnaturalearth::ne_coastline(scale = "medium", returnclass = "sf")
   ## crop the coastlines to the desired range
   if (!is.null(crop_coastlines)) {
     suppressWarnings({
-    coastlines <- st_crop(coastlines, 
-                          xmin = as.numeric(crop_coastlines['lonmin']), 
-                          xmax = as.numeric(crop_coastlines['lonmax']), 
-                          ymin = as.numeric(crop_coastlines['latmin']), 
-                          ymax = as.numeric(crop_coastlines['latmax']))
+      coastlines <- st_crop(coastlines, 
+                            xmin = as.numeric(crop_coastlines['lonmin']), 
+                            xmax = as.numeric(crop_coastlines['lonmax']), 
+                            ymin = as.numeric(crop_coastlines['latmin']), 
+                            ymax = as.numeric(crop_coastlines['latmax']))
     })
   }
   coastlines <- st_transform(coastlines, crs = target_proj) 
-
+  
   if (style == 'polygon') {
     # Calculate polygon points from regular lat/lon
     #NOTE: The original grid must be regular grid with same space
@@ -435,14 +475,14 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     # To prevent out-of-global lat
     lat_poly[which(lat_poly > 90)] <- 90
     lat_poly[which(lat_poly < -90)] <- -90
-
+    
     lonlat_df <- data.frame(lon = lon_poly, lat = lat_poly)
     # Transfer lon/lat to projection
     proj_lonlat <- st_as_sf(lonlat_df, coords = c("lon", "lat"), crs = original_proj)
     #NOTE: if target_proj = "ESRI:54030", on Nord3v2, st_transform has lon and lat swapped!
     proj_lonlat <- st_transform(proj_lonlat, crs = target_proj)
     lonlat_df_proj <- st_coordinates(proj_lonlat)
-
+    
     # Use id to create groups for each polygon
     ids <- factor(paste0("id_", 1:dim(data_df)[1]))
     values <- data.frame(id = ids,
@@ -453,63 +493,63 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     datapoly <- merge(values, positions, by = "id")
     datapoly <- st_as_sf(datapoly, coords = c("x", "y"), crs = target_proj)
     datapoly <- datapoly %>%
-                dplyr::group_by(id) %>%
-                dplyr::summarise() %>%  #NOTE: VERY SLOW if plot global
-                dplyr::mutate(value = values[order(values$id), ]$value) %>%
-                st_cast("POLYGON") %>%
-                st_convex_hull()  # maintain outer polygen (no bowtie shape)
+      dplyr::group_by(.data$id) %>%
+      dplyr::summarise() %>%  #NOTE: VERY SLOW if plot global
+      dplyr::mutate(value = values[order(values$id), ]$value) %>%
+      st_cast("POLYGON") %>%
+      st_convex_hull()  # maintain outer polygen (no bowtie shape)
   }
-
+  
   # Plots
   if (style == 'polygon') {
     res_p <- ggplot(data = data_df) +  #NOTE: must be data_df?
-             geom_sf(data = datapoly,
-                     aes(col = cut(value, breaks = brks_ggplot, include.lowest = T),
-                         fill = cut(value, breaks = brks_ggplot, include.lowest = T)))
+      geom_sf(data = datapoly,
+              aes(col = cut(.data$value, breaks = brks_ggplot, include.lowest = T),
+                  fill = cut(.data$value, breaks = brks_ggplot, include.lowest = T)))
   } else if (style == 'point') {
     res_p <- ggplot(data = data_df) +
-             geom_point(aes(x = long, y = lat,
-                            col = cut(dat, breaks = brks_ggplot, include.lowest = T)),
-                        #NOTE: These two lines make point size vary with lat
-                        #size = point_size /  (data_df$lat / min(data_df$lat))) +
-                        #size = (sort(rep(as.vector(lat), length(lon))) / max(lat)) * point_size) +
-                        size = point_size)
-  }
-
+      geom_point(aes(x = .data$long, y = .data$lat,
+                     col = cut(.data$dat, breaks = brks_ggplot, include.lowest = T)),
+                 #NOTE: These two lines make point size vary with lat
+                 #size = point_size /  (data_df$lat / min(data_df$lat))) +
+                 #size = (sort(rep(as.vector(lat), length(lon))) / max(lat)) * point_size) +
+                 size = point_size)
+  }
+  
   if (is.null(lonlat_df_ori)) {
     coord_sf_lim <- c(range(data_df$long), range(data_df$lat))
   } else {
     coord_sf_lim <- c(range(lonlat_df_ori$long), range(lonlat_df_ori$lat))
   }
   res_p <- res_p +
-           geom_sf(data = coastlines, colour ='black', size = coastlines_width) +
-           # Remove background grid and lat/lon label; add white background
-           theme_void() + theme(plot.background = element_rect(fill = 'white', colour = 'white')) +
-           # crop the projection
-           coord_sf(xlim = coord_sf_lim[1:2], ylim = coord_sf_lim[3:4],
-                    expand = TRUE, datum = target_proj)
-
+    geom_sf(data = coastlines, colour ='black', size = coast_width) +
+    # Remove background grid and lat/lon label; add white background
+    theme_void() + theme(plot.background = element_rect(fill = 'white', colour = 'white')) +
+    # crop the projection
+    coord_sf(xlim = coord_sf_lim[1:2], ylim = coord_sf_lim[3:4],
+             expand = TRUE, datum = target_proj)
+  
   if (!is.null(dots)) {
-    res_p <- res_p + geom_point(data = dots_df, aes(x = long, y = lat),
-                                shape = dots_shape, size = dots_size)
-                                #NOTE: This line makes point size vary with lat
-                                #size = dots_size / (dots_df$lat / min(dots_df$lat)))
+    res_p <- res_p + geom_point(data = dots_df, aes(x = .data$long, y = .data$lat),
+                                shape = dot_symbol, size = dot_size)
+    #NOTE: This line makes point size vary with lat
+    #size = dot_size / (dots_df$lat / min(dots_df$lat)))
   }
-
-  if (identical(legend, 'ggplot2')) {
+  
+  if (identical(drawleg, 'ggplot2')) {
     if (style == 'polygon') {
-    res_p <- res_p + scale_colour_manual(values = cols_ggplot,
-                                         aesthetics = c("colour", "fill"),
-                                         drop = FALSE, na.value = colNA) +
-             guides(fill = guide_legend(title = units, override.aes = list(size = 1)),
-                    color = "none")
-   } else if (style == 'point') {
-    res_p <- res_p + scale_colour_manual(values = cols_ggplot,
-                                         drop = FALSE, na.value = colNA) +
-             guides(colour = guide_legend(title = units, override.aes = list(size = 1)))
-   }
-
-  } else {  # s2dv or NULL
+      res_p <- res_p + scale_colour_manual(values = cols_ggplot,
+                                           aesthetics = c("colour", "fill"),
+                                           drop = FALSE, na.value = colNA) +
+        guides(fill = guide_legend(title = units, override.aes = list(size = 1)),
+               color = "none")
+    } else if (style == 'point') {
+      res_p <- res_p + scale_colour_manual(values = cols_ggplot,
+                                           drop = FALSE, na.value = colNA) +
+        guides(colour = guide_legend(title = units, override.aes = list(size = 1)))
+    }
+    
+  } else {  # bar or NULL
     if (style == 'polygon') {
       res_p <- res_p + scale_colour_manual(values = cols_ggplot,
                                            aesthetics = c("colour", "fill"),
@@ -521,32 +561,32 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     # Remove ggplot legend
     res_p <- res_p + theme(legend.position = "none", plot.margin = margin(0.5, 0, 0, 0, 'cm'))
   }
-
+  
   if (!is.null(toptitle)) {
     res_p <- res_p + ggtitle(toptitle) +
-      theme(plot.title = element_text(size = title_size, hjust = 0.5, vjust = 3))
+      theme(plot.title = element_text(size = title_scale, hjust = 0.5, vjust = 3))
   }
   if (!is.null(caption)) {
     res_p <- res_p + labs(caption = caption) +
       theme(plot.caption = element_text(hjust = 0, vjust = 1, margin = margin(0, 0, 0, 0, 'cm')))
   }
-
-  # s2dv legend fun to put in cowplot::plot_grid
-  if (identical(legend, 's2dv')) {
+  
+  # bar legend fun to put in cowplot::plot_grid
+  if (identical(drawleg, 'bar')) {
     fun_legend <- function() {
       if (vertical) {
         par(mar = c(7.1, 2.2, 7.1, 3.1), mgp = c(3, 1, 0))
       } else {
         par(mar = c(1.1, 1.2, 0.1, 1.1), mgp = c(3, 1, 0))
       }
-      ColorBar(brks = brks, cols = cols, vertical = vertical, subsampleg = NULL,
-               bar_limits = bar_limits, var_limits = var_limits, triangle_ends = triangle_ends,
-               col_inf = col_inf, col_sup = col_sup, color_fun = color_fun,
-               plot = TRUE, draw_ticks = TRUE, draw_separators = FALSE,
-               triangle_ends_scale = 1, extra_labels = NULL,
-               title = units, title_scale = 1, # units_scale
-               label_scale = 1, tick_scale = 1, #bar_tick_scale
-               extra_margin = bar_extra_margin, label_digits = 4)
+      ColorBarContinuous(brks = brks, cols = cols, vertical = vertical, subsampleg = NULL,
+                         bar_limits = bar_limits, var_limits = var_limits, triangle_ends = triangle_ends,
+                         col_inf = col_inf, col_sup = col_sup, color_fun = color_fun,
+                         plot = TRUE, draw_bar_ticks = TRUE, draw_separators = FALSE,
+                         triangle_ends_scale = 1, bar_extra_labels = NULL,
+                         title = units, title_scale = 1, # units_scale
+                         bar_label_scale = 1, bar_tick_scale = 1,
+                         bar_extra_margin = bar_extra_margin, bar_label_digits = 4)
     }
     if (vertical) {
       res_p <- cowplot::plot_grid(res_p, fun_legend, rel_widths = c(6, 1))
@@ -555,7 +595,7 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     }
     res_p <- res_p +  theme(plot.background = element_rect(fill = "white", colour = "white"))
   }
-
+  
   if (!is.null(fileout)) {
     ext <- regmatches(fileout, regexpr("[a-zA-Z0-9]*$", fileout))
     ggsave(fileout, res_p, width = width, height = height, dpi = res, units = size_units, 
@@ -564,6 +604,6 @@ PlotRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     dev.new(units = size_units, res = res, width = width, height = height)
     res_p 
   } 
-
+  
 }
 
-- 
GitLab