From 2e2f03ebf70feaeaa50890de4cc1170369630d0f Mon Sep 17 00:00:00 2001
From: effingpaul <effingpaul@tu-berlin.de>
Date: Thu, 9 Feb 2023 19:11:31 +0100
Subject: [PATCH 1/2] added mapAreaPattern.R

---
 DESCRIPTION        |   3 +-
 NAMESPACE          |   1 +
 R/mipAreaPattern.R | 232 +++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 235 insertions(+), 1 deletion(-)
 create mode 100644 R/mipAreaPattern.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 3ec8795..878bff5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -36,7 +36,8 @@ Imports:
     rlang,
     shiny,
     tidyr,
-    trafficlight
+    trafficlight,
+	ggpattern
 Suggests: 
     covr,
     gdxrrw,
diff --git a/NAMESPACE b/NAMESPACE
index 6f29175..6a576f0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,6 +3,7 @@
 export(extractVariableGroups)
 export(getPlotData)
 export(mipArea)
+export(mipAreaPattern)
 export(mipBarYearData)
 export(mipIterations)
 export(mipLineHistorical)
diff --git a/R/mipAreaPattern.R b/R/mipAreaPattern.R
new file mode 100644
index 0000000..ba402c0
--- /dev/null
+++ b/R/mipAreaPattern.R
@@ -0,0 +1,232 @@
+#' Generic area plot function. Automatically creates facet grid from data. Optionally adds total line. Supports patterns.
+#'
+#' @param x Data to plot. Allowed data formats: magpie or quitte. NOTE: To ensure correct conversion to quitte objects,
+#' the dimension that contains the variables must have one of the following names: variable, scenario, or model.
+#' @param stack_priority Name of column you want to stack. If you provide more than one column name the
+#' function will scan the columns in the given order and use the first dimension for stacking that has
+#' more than one element.
+#' @param total total data to plot. Allowed inputs: magpie, quitte or boolean. If total data is
+#' provided by user in magpie or quitte format it will be added to the plot. If user sets total to
+#' TRUE total will be calculated by the function and added to the plot. If total is FALSE the plot
+#' will ignore it.
+#' @param scales scales can be fixed ("fixed", default), free ("free"), or free in one dimension ("free_x", "free_y")?
+#' @param shorten Shorten variable names (default is TRUE) by removing categories only if they are identical (for short
+#' names in the legend)
+#' @param hist Historical data. Allowed data formats: magpie or quitte. NOTE: To ensure correct conversion to quitte
+#' objects, the dimension that contains the variables must have one of the following names: variable, scenario, model.
+#' @param hist_source If there are multiple historical sources the name of the source that you want to be plotted.
+#' @param patternDensity Sets globally the density of all patterns
+#' @param patternKeyScale Sets globally the size of all patterns in the legend items
+#' @author David Klein, Jan Philipp Dietrich, Paul Effing
+#' @section Example Plot:
+#' \if{html}{\figure{mipAreaPattern.png}{example plot}}
+#' @examples
+#' p <- mipAreaPattern(x = mip_example_data)
+#' # create plot with best-guess design (internally using theme_mip(size=12))
+#' p <- mipAreaPattern(mip_example_data)
+#' # override default theme with theme_grey and move legend to top
+#' library(ggplot2)
+#' p <- p + theme_grey() + theme(legend.position = "top")
+#' # go back to theme_mip and increase font size
+#' p <- p + theme_mip(size = 18)
+#' # change facetting
+#' p <- p + facet_grid(region ~ scenario)
+#' @importFrom magclass is.magpie getSets
+#' @importFrom quitte is.quitte
+#' @importFrom ggplot2 ggplot geom_area_pattern aes_ geom_line scale_linetype_discrete
+#'   facet_wrap facet_grid theme scale_fill_manual xlab expand_limits
+#' @importFrom dplyr group_by summarise ungroup
+#' @importFrom rlang .data
+#' @importFrom ggpattern
+#' @export
+mipAreaPattern <- function(x, stack_priority = c("variable", "region"), total = TRUE, scales = "fixed", shorten = TRUE, #nolint
+                    hist = NULL, hist_source = "first", patternDensity = 0.35, patternKeyScale =0.6) { #nolint
+  ############################################
+  ######  P R E P A R E   D A T A  ###########
+  ############################################
+
+  # To ensure correct conversion to quitte objects, there should be at least
+  # one dimension named "variable" or "scenario" or "model" in MAgPIE objects.
+  if (is.magpie(x) & !any(c("variable", "model", "scenario") %in% getSets(x))) {
+    stop("MAgPIE objects need to have at least one dimension named 'variable' or 'model' or 'scenario'.")
+  }
+
+  x <- as.quitte(x)
+
+  # Add dummy scenario if data does not contain a scenario
+  # Otherwise selecting all scenarios that are not 'historicl' further down deletes ALL data
+  if (all(is.na(x$scenario))) x$scenario <- "default"
+
+  # shorten variable names and calc ylab
+  if (shorten) x$variable <- shorten_legend(x$variable, identical_only = TRUE)
+  ylab <- paste0(sub(".$", "", attr(x$variable, "front")), attr(x$variable, "back"))
+  # add unit
+  unit <- unique(as.character(x$unit))
+  ylab <- paste0(ylab, " (", paste0(unit, collapse = " | "), ")")
+
+  # Repeat the same for history
+  if (!is.null(hist)) {
+    if (is.magpie(hist) & !any(c("variable", "model", "scenario") %in% getSets(hist))) {
+      stop("MAgPIE objects with historical data need to have at least one dimension named 'variable' or 'model' or ",
+           "'scenario'.")
+    }
+    hist <- as.quitte(hist)
+    if (shorten) hist$variable <- shorten_legend(hist$variable, identical_only = TRUE)
+    # select historical data source
+    if (hist_source == "first") {
+      hist <- hist[hist$model == levels(hist$model)[1], ]
+    } else if (hist_source %in% levels(hist$model)) {
+      hist <- hist[hist$model == hist_source, ]
+    } else {
+      warning(paste0(hist_source, " could not be found in the historical data!"))
+      hist <- NULL
+    }
+  }
+
+  ###
+  ### Find out which variables to stack and which to put to facet_grid
+  ###
+
+  # count levels of the given columns
+  nLevels <- vapply(subset(x, select = c("variable", "region", "scenario", "model")), nlevels, integer(1))
+
+  # Find first dimension in stack_priority that has more than one element.
+  # Initialize dimToStack (this applies if if all dimensions have only one element)
+  dimToStack <- stack_priority[1]
+  for (s in stack_priority) {
+    if (nLevels[s] > 1) {
+      dimToStack <- s
+      break
+    }
+  }
+
+  # find and sort dimension with more than one element, exclude dimToStack
+  # sort: to be able to build the interaction with the smallest number of resulting combinations (further down)
+  facets <- sort(nLevels[nLevels > 1])
+  facets <- setdiff(names(facets), dimToStack)
+
+  # Combine data and historical data into one object
+  if (!is.null(hist)) x <- rbind(x, hist)
+
+  # if there are three facet dimensions that have more than one element combine the two
+  # smallest ones into the first one to be able to create a 2-D facet_grid later on
+  if (length(facets) == 3) {
+    x[, facets[1]] <- interaction(x[[facets[1]]], x[[facets[2]]])
+  }
+
+  # if not provided by user calculate total by summing over dimToStack
+  if (isTRUE(total)) {
+    dimToGroup <- setdiff(c("model", "scenario", "region", "variable", "unit", "period"), dimToStack)
+    total <- x %>%
+      group_by(.data[[dimToGroup[1]]], .data[[dimToGroup[2]]], .data[[dimToGroup[3]]],
+               .data[[dimToGroup[4]]], .data[[dimToGroup[5]]]) %>%
+      summarise(value = sum(.data[["value"]], na.rm = TRUE)) %>%
+      ungroup()
+    # add missing column dimToStack to make it convertable to quitte
+    total[, dimToStack] <- "Total"
+  }
+
+  # convert total to quitte
+  if (!identical(FALSE, total)) total <- as.quitte(total)
+
+  # separate positive and negative parts of data for area plot
+  tmp <- droplevels(x[x$scenario != "historical", ])
+
+  pos <- tmp
+  neg <- tmp
+
+  pos$value <- ifelse(tmp$value >= 0, tmp$value, 0)
+  neg$value <- ifelse(tmp$value < 0, tmp$value, -1e-36)
+
+  if (!is.null(hist)) {
+    tmp <- droplevels(x[x$scenario == "historical", ])
+    postmp <- tmp
+    negtmp <- tmp
+
+    postmp$value <- ifelse(tmp$value >= 0, tmp$value, 0)
+    negtmp$value <- ifelse(tmp$value < 0, tmp$value, -1e-36)
+
+    posH <- NULL
+    negH <- NULL
+
+    # repeat historical data as often as there are scenarios
+    # so that they will be plotted for each single scenario
+    for (l in levels(pos$scenario)) {
+      postmp$scenario <- factor(l)
+      negtmp$scenario <- factor(l)
+
+      posH <- rbind(posH, postmp)
+      negH <- rbind(negH, negtmp)
+    }
+  }
+
+  # split historical and model total
+  if (!identical(FALSE, total)) {
+    totalX <- droplevels(total[total$scenario != "historical", ])
+  }
+
+  if (!is.null(hist) & !identical(FALSE, total)) {
+    tottmp <- droplevels(total[total$scenario == "historical", ])
+    # repeat historical total as often as there are scenarios
+    # so that it will be plotted for each single scenario
+    totalH <- NULL
+    for (l in levels(pos$scenario)) {
+      tottmp$scenario <- factor(l)
+      totalH <- rbind(totalH, tottmp)
+    }
+  }
+
+  ############################################
+  ###############  P L O T  ##################
+  ############################################
+
+  p <- ggplot() +
+    geom_area_pattern(data = pos, aes_(~period, ~value, pattern = as.formula(paste("~", dimToStack)), fill = as.formula(paste("~", dimToStack)), pattern_spacing = as.formula(paste("~", dimToStack))), pattern_density = patternDensity, pattern_key_scale_factor = patternKeyScale) +
+    geom_area_pattern(data = neg, aes_(~period, ~value, pattern = as.formula(paste("~", dimToStack)), fill = as.formula(paste("~", dimToStack)), pattern_spacing = as.formula(paste("~", dimToStack))), pattern_density = patternDensity, pattern_key_scale_factor = patternKeyScale)
+
+  if (!is.null(hist)) {
+    p <- p + geom_area_pattern(data = posH, aes_(~period, ~value, pattern = as.formula(paste("~", dimToStack)), fill = as.formula(paste("~", dimToStack)), pattern_spacing = as.formula(paste("~", dimToStack))), pattern_density = patternDensity, pattern_key_scale_factor = patternKeyScale, alpha = 0.3)
+    p <- p + geom_area_pattern(data = negH, aes_(~period, ~value, pattern = as.formula(paste("~", dimToStack)), fill = as.formula(paste("~", dimToStack)), pattern_spacing = as.formula(paste("~", dimToStack))), pattern_density = patternDensity, pattern_key_scale_factor = patternKeyScale, alpha = 0.3)
+  }
+
+
+  # define facet_grid
+  if (length(facets) == 1) p <- p + facet_wrap(as.formula(paste("~", facets)), scales = scales)
+  if (length(facets) == 2) p <- p + facet_grid(as.formula(paste(facets[1], "~", facets[2])), scales = scales)
+  # facet 1 and 2 are combined in dim 1
+  if (length(facets) == 3) p <- p + facet_grid(as.formula(paste(facets[1], "~", facets[3])), scales = scales)
+
+  # add total to plot as black line
+  if (is.quitte(total)) {
+    p <- p + geom_line(data = totalX, aes_(~period, ~value, linetype = as.formula(paste("~", dimToStack))),
+                       color = "#000000", size = 1)
+    p <- p + scale_linetype_discrete(labels = "Total", name = "")
+    if (!is.null(hist)) {
+      p <- p + geom_line(data = totalH, aes_(~period, ~value, linetype = as.formula(paste("~", dimToStack))),
+                         color = "#000000", size = 1, alpha = 0.3)
+    }
+  }
+
+  # plot settings
+  p <- p + xlab("Year")
+  p <- p + ylab(ylab)
+
+  # update theme
+  p <- p + theme_minimal()
+  p <- p + theme_mip(size = 12)
+  p <- p + theme(axis.title.x = element_blank())
+
+  # If data that is to be stacked are not factors, convert it to factors.
+  # This is useful since we can use the same call of plotstyle as in other mip functions and thus
+  # get the same order of colors for elements that are not defined in plotstyle.
+  if (!is.factor(x[[dimToStack]])) x[[dimToStack]] <- factor(x[[dimToStack]], levels = unique(x[[dimToStack]]))
+  # because of conflicts with patterns, dont use plotstyle colours and labels by default
+  # p <- p + scale_fill_manual(values = plotstyle(levels(x[[dimToStack]])),
+  #                          name   = "")
+
+  # increase y-axis limits to hide all-zero data that was set to -1e-36
+  p <- p +
+    expand_limits(y = c(-1, 1) * 1e-32)
+
+  return(p)
+}

From 15ee20e50604d82f40d9ab86d9131fa8cb7c1f0a Mon Sep 17 00:00:00 2001
From: effingpaul <effingpaul@tu-berlin.de>
Date: Wed, 15 Feb 2023 02:17:28 +0100
Subject: [PATCH 2/2] added documentation

---
 NAMESPACE             |  3 ++
 R/mipAreaPattern.R    | 16 ++++++---
 man/mipAreaPattern.Rd | 76 +++++++++++++++++++++++++++++++++++++++++++
 mif.Rmd               |  0
 4 files changed, 91 insertions(+), 4 deletions(-)
 create mode 100644 man/mipAreaPattern.Rd
 create mode 100644 mif.Rmd

diff --git a/NAMESPACE b/NAMESPACE
index 6a576f0..cca1eeb 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -45,6 +45,9 @@ importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(dplyr,sym)
 importFrom(dplyr,ungroup)
+importFrom(ggpattern,geom_area_pattern)
+importFrom(ggpattern,scale_pattern_manual)
+importFrom(ggpattern,scale_pattern_spacing_manual)
 importFrom(ggplot2,"%+replace%")
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_)
diff --git a/R/mipAreaPattern.R b/R/mipAreaPattern.R
index ba402c0..7c269c6 100644
--- a/R/mipAreaPattern.R
+++ b/R/mipAreaPattern.R
@@ -31,13 +31,21 @@
 #' p <- p + theme_mip(size = 18)
 #' # change facetting
 #' p <- p + facet_grid(region ~ scenario)
+#'
+#' # patterns and color scales can be added manually here:
+#' # p <- p + scale_pattern_manual(values = patternValues,
+#'                      labels = labels) +
+#' # p <- p + scale_pattern_spacing_manual(values= spacingValues,
+#'                                labels = labels)+
+#' # p <- p + scale_fill_manual(values=colorFillValues,
+#'                     labels = labels)
 #' @importFrom magclass is.magpie getSets
 #' @importFrom quitte is.quitte
-#' @importFrom ggplot2 ggplot geom_area_pattern aes_ geom_line scale_linetype_discrete
+#' @importFrom ggplot2 ggplot aes_ geom_line scale_linetype_discrete
 #'   facet_wrap facet_grid theme scale_fill_manual xlab expand_limits
 #' @importFrom dplyr group_by summarise ungroup
 #' @importFrom rlang .data
-#' @importFrom ggpattern
+#' @importFrom ggpattern geom_area_pattern scale_pattern_manual scale_pattern_spacing_manual
 #' @export
 mipAreaPattern <- function(x, stack_priority = c("variable", "region"), total = TRUE, scales = "fixed", shorten = TRUE, #nolint
                     hist = NULL, hist_source = "first", patternDensity = 0.35, patternKeyScale =0.6) { #nolint
@@ -221,8 +229,8 @@ mipAreaPattern <- function(x, stack_priority = c("variable", "region"), total =
   # get the same order of colors for elements that are not defined in plotstyle.
   if (!is.factor(x[[dimToStack]])) x[[dimToStack]] <- factor(x[[dimToStack]], levels = unique(x[[dimToStack]]))
   # because of conflicts with patterns, dont use plotstyle colours and labels by default
-  # p <- p + scale_fill_manual(values = plotstyle(levels(x[[dimToStack]])),
-  #                          name   = "")
+  p <- p + scale_pattern_manual(values= rep("none", length(unique(x[[dimToStack]])))) +
+           scale_pattern_spacing_manual(values= rep(0.0, length(unique(x[[dimToStack]]))))
 
   # increase y-axis limits to hide all-zero data that was set to -1e-36
   p <- p +
diff --git a/man/mipAreaPattern.Rd b/man/mipAreaPattern.Rd
new file mode 100644
index 0000000..218f31d
--- /dev/null
+++ b/man/mipAreaPattern.Rd
@@ -0,0 +1,76 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mipAreaPattern.R
+\name{mipAreaPattern}
+\alias{mipAreaPattern}
+\title{Generic area plot function. Automatically creates facet grid from data. Optionally adds total line. Supports patterns.}
+\usage{
+mipAreaPattern(
+  x,
+  stack_priority = c("variable", "region"),
+  total = TRUE,
+  scales = "fixed",
+  shorten = TRUE,
+  hist = NULL,
+  hist_source = "first",
+  patternDensity = 0.35,
+  patternKeyScale = 0.6
+)
+}
+\arguments{
+\item{x}{Data to plot. Allowed data formats: magpie or quitte. NOTE: To ensure correct conversion to quitte objects,
+the dimension that contains the variables must have one of the following names: variable, scenario, or model.}
+
+\item{stack_priority}{Name of column you want to stack. If you provide more than one column name the
+function will scan the columns in the given order and use the first dimension for stacking that has
+more than one element.}
+
+\item{total}{total data to plot. Allowed inputs: magpie, quitte or boolean. If total data is
+provided by user in magpie or quitte format it will be added to the plot. If user sets total to
+TRUE total will be calculated by the function and added to the plot. If total is FALSE the plot
+will ignore it.}
+
+\item{scales}{scales can be fixed ("fixed", default), free ("free"), or free in one dimension ("free_x", "free_y")?}
+
+\item{shorten}{Shorten variable names (default is TRUE) by removing categories only if they are identical (for short
+names in the legend)}
+
+\item{hist}{Historical data. Allowed data formats: magpie or quitte. NOTE: To ensure correct conversion to quitte
+objects, the dimension that contains the variables must have one of the following names: variable, scenario, model.}
+
+\item{hist_source}{If there are multiple historical sources the name of the source that you want to be plotted.}
+
+\item{patternDensity}{Sets globally the density of all patterns}
+
+\item{patternKeyScale}{Sets globally the size of all patterns in the legend items}
+}
+\description{
+Generic area plot function. Automatically creates facet grid from data. Optionally adds total line. Supports patterns.
+}
+\section{Example Plot}{
+
+\if{html}{\figure{mipAreaPattern.png}{example plot}}
+}
+
+\examples{
+p <- mipAreaPattern(x = mip_example_data)
+# create plot with best-guess design (internally using theme_mip(size=12))
+p <- mipAreaPattern(mip_example_data)
+# override default theme with theme_grey and move legend to top
+library(ggplot2)
+p <- p + theme_grey() + theme(legend.position = "top")
+# go back to theme_mip and increase font size
+p <- p + theme_mip(size = 18)
+# change facetting
+p <- p + facet_grid(region ~ scenario)
+
+# patterns and color scales can be added manually here:
+# p <- p + scale_pattern_manual(values = patternValues,
+                     labels = labels) +
+# p <- p + scale_pattern_spacing_manual(values= spacingValues,
+                               labels = labels)+
+# p <- p + scale_fill_manual(values=colorFillValues,
+                    labels = labels)
+}
+\author{
+David Klein, Jan Philipp Dietrich, Paul Effing
+}
diff --git a/mif.Rmd b/mif.Rmd
new file mode 100644
index 0000000..e69de29