multiplots with patchwork

DESCRIPTION

@@ -1,14 +1,13 @@
 Package: jaspGraphs
 Type: Package
 Title: Custom Graphs for JASP
-Version: 0.19.0
+Version: 0.19.0.9000
 Author: Don van den Bergh
 Maintainer: JASP-team <info@jasp-stats.nl>
 Description: Graph making functions and wrappers for JASP.
 License: GPL
 Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: testthat
 Imports: 
     ggplot2 (>= 3.0.0),
@@ -20,5 +19,6 @@ Imports:
     RColorBrewer,
     rlang,
     scales,
-    viridisLite
+    viridisLite,
+    patchwork
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,19 +1,33 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("$",Enum)
 S3method("[[",jaspGraphsPlot)
 S3method("[[<-",jaspGraphsPlot)
 S3method(getAxisBreaks,gg)
 S3method(getAxisBreaks,ggplot)
 S3method(getAxisBreaks,ggplot_built)
 S3method(getAxisBreaks,list)
+S3method(getAxisInfo,ScaleContinuousPosition)
+S3method(getAxisInfo,ScaleDiscretePosition)
+S3method(getPlotEditingOptions,"function")
+S3method(getPlotEditingOptions,default)
+S3method(getPlotEditingOptions,gg)
+S3method(getPlotEditingOptions,ggplot)
+S3method(getPlotEditingOptions,ggplot_built)
+S3method(getPlotEditingOptions,jaspGraphsPlot)
+S3method(getPlotEditingOptions,qgraph)
 S3method(getPrettyAxisBreaks,character)
 S3method(getPrettyAxisBreaks,default)
 S3method(getPrettyAxisBreaks,factor)
 S3method(getPrettyAxisBreaks,numeric)
 S3method(ggMatrixPlot,default)
 S3method(ggMatrixPlot,list)
 S3method(ggMatrixPlot,matrix)
+S3method(internalUpdateAxis,ScaleContinuousPosition)
+S3method(internalUpdateAxis,ScaleDiscretePosition)
 S3method(length,jaspGraphsPlot)
+S3method(makeLabels,default)
+S3method(makeLabels,list)
 S3method(names,jaspGraphsPlot)
 S3method(needsParsing,character)
 S3method(needsParsing,data.frame)
@@ -24,7 +38,11 @@ S3method(plot,jaspGraphs)
 S3method(plot,jaspGraphsPlot)
 S3method(print,jaspGraphs)
 S3method(print,jaspGraphsPlot)
+export(.densityArgs)
 export(.graphOptions)
+export(.histogramArgs)
+export(.marginalArgs)
+export(.rugArgs)
 export(GeomAbline2)
 export(GeomAlignedText)
 export(GeomRangeFrame)
@@ -53,7 +71,11 @@ export(ggMatrixPlot)
 export(graphOptions)
 export(hypothesis2BFtxt)
 export(is.jaspGraphsPlot)
+export(jaspBivariate)
+export(jaspBivariateWithMargins)
 export(jaspHistogram)
+export(jaspMarginal)
+export(jaspMatrixPlot)
 export(needsParsing)
 export(parseThis)
 export(plotEditing)
@@ -71,6 +93,8 @@ export(themeApaRaw)
 export(themeJasp)
 export(themeJaspRaw)
 export(themePubrRaw)
+importFrom(R6,R6Class)
+importFrom(RColorBrewer,brewer.pal)
 importFrom(ggplot2,.pt)
 importFrom(ggplot2,ScaleContinuousPosition)
 importFrom(ggplot2,aes)
@@ -120,3 +144,4 @@ importFrom(gtable,gtable_add_padding)
 importFrom(gtable,gtable_add_rows)
 importFrom(rlang,.data)
 importFrom(scales,censor)
+importFrom(viridisLite,viridis)

R/JASPScatterPlot.R

@@ -1,7 +1,7 @@
 #' @importFrom ggplot2 geom_smooth theme_void geom_ribbon
 #' @importFrom rlang .data
 
-#' @title Create a scatter plot with density
+#' @title DEPRECATED, use [jaspBivariateWithMargins] instead. Create a scatter plot with density
 #'
 #' @param x x variable.
 #' @param y y variable.
@@ -19,6 +19,8 @@
 #' @param showLegend Should the legend be shown?
 #' @param legendTitle A string for the title of the legend. \code{NULL} implies the legend is not shown.
 #' @param emulateGgMarginal Should the result be as similar as possible to \code{\link[ggExtra]{ggMarginal}}? Overwrites other parameters.
+#' @param plotComposer, String, should "gridExtra" or "patchwork" be used for combining plots?
+#' @param legendPosition where should the legend position be placed? "topRightPatch",
 #' @param ... passed to \code{\link{themeJaspRaw}}.
 #'
 #' @details The only change added when \code{emulateGgMarginal = TRUE} is that \code{ggplot2::theme(plot.margin = unit(c(0, 0, 0.25, 0.25), "cm"))}
@@ -37,8 +39,16 @@ JASPScatterPlot <- function(x, y, group = NULL, xName = NULL, yName = NULL,
                             showLegend = !is.null(group),
                             legendTitle = NULL,
                             emulateGgMarginal = FALSE,
+                            plotComposer = c("gridExtra", "patchwork"),
+                            legendPosition = "topRightPatch",
                             ...) {
 
+  lifecycle::deprecate_warn(
+    "0.19.0.9000",
+    "JASPScatterPlot()",
+    "jaspBivariateWithMargins()"
+  )
+
   # TODO: make actual error messages
   stopifnot(
     is.numeric(x),
@@ -53,6 +63,7 @@ JASPScatterPlot <- function(x, y, group = NULL, xName = NULL, yName = NULL,
   )
   plotAbove <- match.arg(plotAbove)
   plotRight <- match.arg(plotRight)
+  plotComposer  <- match.arg(plotComposer)
 
   # can't make a legend without group
   showLegend <- showLegend && !is.null(group)
@@ -76,7 +87,7 @@ JASPScatterPlot <- function(x, y, group = NULL, xName = NULL, yName = NULL,
 
   dots <- list(...)
   if (showLegend)
-    dots <- setDefaults(dots, legend.position = "right")
+    dots <- setDefaults(dots, legend.position = if (identical(legendPosition, "topRightPatch")) "right" else legendPosition)
 
   mainPlot <- ggplot(df, mapping) +
     geom_point() +
@@ -99,16 +110,41 @@ JASPScatterPlot <- function(x, y, group = NULL, xName = NULL, yName = NULL,
   topPlot   <- JASPScatterSubPlot(x, group, plotAbove, x.range, colorAreaUnderDensity, alphaAreaUnderDensity)
   rightPlot <- JASPScatterSubPlot(y, group, plotRight, y.range, colorAreaUnderDensity, alphaAreaUnderDensity, flip = TRUE)
 
-  plotList <- list(mainPlot = mainPlot, topPlot = topPlot, rightPlot = rightPlot)
-  plotList <- plotList[lengths(plotList) > 0L]
+  if (plotComposer == "patchwork") {
 
-  plot <- jaspGraphsPlot$new(
-    subplots     = plotList,
-    plotFunction = reDrawAlignedPlot,
-    size         = 5,
-    showLegend   = showLegend
-  )
-  return(plot)
+    topRightPatch <- if (is.null(topPlot)) {
+      NULL
+    } else if (identical(legendPosition, "topRightPatch")) {
+       patchwork::guide_area()
+    } else {
+      patchwork::plot_spacer()
+    }
+    noLegend <- theme(legend.position = "none")
+    extraLegend <- if (identical(legendPosition, "topRightPatch")) NULL else theme(legend.position = legendPosition)
+
+    plot <-
+      (topPlot + noLegend) + topRightPatch          +
+      mainPlot             + (rightPlot + noLegend) +
+      patchwork::plot_layout(
+        widths  = c(1, 1 / 5),
+        heights = c(1 / 5, 1),
+        guides  = "collect"
+      ) & extraLegend
+    return(plot)
+
+  } else {
+
+    plotList <- list(mainPlot = mainPlot, topPlot = topPlot, rightPlot = rightPlot)
+    plotList <- plotList[lengths(plotList) > 0L]
+
+    plot <- jaspGraphsPlot$new(
+      subplots     = plotList,
+      plotFunction = reDrawAlignedPlot,
+      size         = 5,
+      showLegend   = showLegend
+    )
+    return(plot)
+  }
 }
 
 JASPScatterSubPlot <- function(x, group = NULL, type = c("density", "histogram", "none"), range,
@@ -129,7 +165,7 @@ JASPScatterSubPlot <- function(x, group = NULL, type = c("density", "histogram",
     foo <- function(x, ...) as.data.frame(stats::density(x, from = range[1L], to = range[2L])[c("x", "y")])
     geom <- geom_line(linewidth = 0.5, show.legend = FALSE)
     geom2 <- if (colorAreaUnderDensity) {
-      geom_ribbon(aes(ymin = 0, ymax = .data$y), alpha = alpha)
+      geom_ribbon(aes(ymin = 0, ymax = .data$y), alpha = alpha, show.legend = FALSE)
     } else {
       NULL
     }

R/JASPgraphsPlot.R

@@ -1,5 +1,8 @@
 #' @importFrom ggplot2 is.ggplot
 
+# silences a note in the R CMD Check but is not strictly necessary
+#'@importFrom R6 R6Class
+
 jaspGraphsPlot <- R6::R6Class(
   classname = "jaspGraphsPlot",
   public = list(

R/colorPalettes.R

@@ -1,6 +1,10 @@
 
 #'@importFrom ggplot2 continuous_scale discrete_scale
 
+# these two silence a note in the R CMD Check but are not strictly necessary
+#'@importFrom viridisLite viridis
+#'@importFrom RColorBrewer brewer.pal
+
 jaspGraphs_data <- list2env(list(
   # discrete color scales
   colorblind     = list(colors = RColorBrewer::brewer.pal(8L, "Dark2")),

R/customGeoms.R

@@ -1,3 +1,4 @@
+#'@importFrom ggplot2 aes
 
 setDefaults <- function(lst, ...) {
 
@@ -23,7 +24,7 @@ setDefaults <- function(lst, ...) {
 jaspGeomPoint <- ggplot2::ggproto(
 	`_class`    = "jaspGeomPoint",
 	`_inherit`  = ggplot2::GeomPoint,
-	default_aes = aes(size = 3, shape = 21, colour = "black", fill = "grey", alpha = NA, stroke = 0.5)
+	default_aes = ggplot2::aes(size = 3, shape = 21, colour = "black", fill = "grey", alpha = NA, stroke = 0.5)
 )
 
 #' @title Custom geoms
@@ -51,7 +52,7 @@ geom_point <- function(mapping = NULL, data = NULL, stat = "identity", position
 jaspGeomLine <- ggplot2::ggproto(
   `_class`    = "jaspGeomLine",
   `_inherit`  = ggplot2::GeomLine,
-  default_aes = aes(linewidth = 1.00, colour = "black", linetype = 1, alpha = NA)
+  default_aes = ggplot2::aes(linewidth = 1.00, colour = "black", linetype = 1, alpha = NA)
 )
 
 #' @rdname geom_point

R/enums.R

@@ -12,6 +12,7 @@ createEnum <- function(nameValuePairs) {
   e
 }
 
+#' @exportS3Method "$" Enum
 `$.Enum` <- function(x, y) {
   out <- NextMethod(x, y)
   if (is.null(out)) stop2(sprintf("nonexisting enum type %s!", y))

R/geom_rangeframe.R

@@ -207,7 +207,7 @@ GeomRangeFrame <- ggplot2::ggproto("GeomRangeFrame", ggplot2::Geom,
     }
     ggname("geom_rangeframe", gTree(children = do.call("gList", rugs)))
   },
-  default_aes = aes(colour = "black", size = 0.5, linetype = 1, alpha = NA),
+  default_aes = ggplot2::aes(colour = "black", size = 0.5, linetype = 1, alpha = NA),
 
   draw_key = ggplot2::draw_key_path
 )

R/ggMatrixPlot.R

@@ -30,6 +30,7 @@ makeLabels <- function(label, angle = 0, size = 1, family = graphOptions("family
   UseMethod("makeLabels", label)
 }
 
+#' @exportS3Method
 makeLabels.default <- function(label, angle = 0, size = 1, family = graphOptions("family"),
                                vjust = "center", hjust = "center", x = .5, y = .5) {
 
@@ -70,6 +71,7 @@ makeLabels.default <- function(label, angle = 0, size = 1, family = graphOptions
   }
 }
 
+#' @exportS3Method
 makeLabels.list <- function(label, angle = 0, size = 1, family = graphOptions("family"),
                             vjust = "center", hjust = "center", x = .5, y = .5) {
 
@@ -385,6 +387,13 @@ ggMatrixPlot.default <- function(plotList = NULL, nr = NULL, nc = NULL,
                                  scaleXYlabels  = c(.9,.9),
                                  debug          = FALSE) {
 
+  lifecycle::deprecate_warn(
+    "0.19.0.9000",
+    "jaspGraphs::ggMatrixPlot(...)",
+    "jaspGraphs::jaspMatrixPlot(...)",
+    details = "jaspMatrixPlot supersedes ggMatrixPlot."
+  )
+
   removeXYlabels <- match.arg(removeXYlabels)
   if (is.null(plotList) && debug) {