diff stat_bag.r @ 2:c29354d16967 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stat_bag.r	Mon Aug 13 04:55:07 2018 -0400
@@ -0,0 +1,145 @@
+library(ggplot2)
+StatBag <- ggproto("Statbag", Stat,
+                   compute_group = function(data, scales, prop = 0.5) {
+
+                     #################################
+                     #################################
+                     # originally from aplpack package, plotting functions removed
+                     plothulls_ <- function(x, y, fraction, n.hull = 1,
+                                            col.hull, lty.hull, lwd.hull, density=0, ...){
+                       # function for data peeling:
+                       # x,y : data
+                       # fraction.in.inner.hull : max percentage of points within the hull to be drawn
+                       # n.hull : number of hulls to be plotted (if there is no fractiion argument)
+                       # col.hull, lty.hull, lwd.hull : style of hull line
+                       # plotting bits have been removed, BM 160321
+                       # pw 130524
+                       if(ncol(x) == 2){ y <- x[,2]; x <- x[,1] }
+                       n <- length(x)
+                       if(!missing(fraction)) { # find special hull
+                         n.hull <- 1
+                         if(missing(col.hull)) col.hull <- 1
+                         if(missing(lty.hull)) lty.hull <- 1
+                         if(missing(lwd.hull)) lwd.hull <- 1
+                         x.old <- x; y.old <- y
+                         idx <- chull(x,y); x.hull <- x[idx]; y.hull <- y[idx]
+                         for( i in 1:(length(x)/3)){
+                           x <- x[-idx]; y <- y[-idx]
+                           if( (length(x)/n) < fraction ){
+                             return(cbind(x.hull,y.hull))
+                           }
+                           idx <- chull(x,y); x.hull <- x[idx]; y.hull <- y[idx];
+                         }
+                       }
+                       if(missing(col.hull)) col.hull <- 1:n.hull
+                       if(length(col.hull)) col.hull <- rep(col.hull,n.hull)
+                       if(missing(lty.hull)) lty.hull <- 1:n.hull
+                       if(length(lty.hull)) lty.hull <- rep(lty.hull,n.hull)
+                       if(missing(lwd.hull)) lwd.hull <- 1
+                       if(length(lwd.hull)) lwd.hull <- rep(lwd.hull,n.hull)
+                       result <- NULL
+                       for( i in 1:n.hull){
+                         idx <- chull(x,y); x.hull <- x[idx]; y.hull <- y[idx]
+                         result <- c(result, list( cbind(x.hull,y.hull) ))
+                         x <- x[-idx]; y <- y[-idx]
+                         if(0 == length(x)) return(result)
+                       }
+                       result
+                     } # end of definition of plothulls
+                     #################################
+
+
+                     # prepare data to go into function below
+                     the_matrix <- matrix(data = c(data$x, data$y), ncol = 2)
+
+                     # get data out of function as df with names
+                     setNames(data.frame(plothulls_(the_matrix, fraction = prop)), nm = c("x", "y"))
+                     # how can we get the hull and loop vertices passed on also?
+                   },
+
+                   required_aes = c("x", "y")
+)
+
+#' @inheritParams ggplot2::stat_identity
+#' @param prop Proportion of all the points to be included in the bag (default is 0.5)
+stat_bag <- function(mapping = NULL, data = NULL, geom = "polygon",
+                     position = "identity", na.rm = FALSE, show.legend = NA, 
+                     inherit.aes = TRUE, prop = 0.5, alpha = 0.3, ...) {
+  layer(
+    stat = StatBag, data = data, mapping = mapping, geom = geom, 
+    position = position, show.legend = show.legend, inherit.aes = inherit.aes,
+    params = list(na.rm = na.rm, prop = prop, alpha = alpha, ...)
+  )
+}
+
+
+geom_bag <- function(mapping = NULL, data = NULL,
+                     stat = "identity", position = "identity",
+                     prop = 0.5, 
+                     alpha = 0.3,
+                     ...,
+                     na.rm = FALSE,
+                     show.legend = NA,
+                     inherit.aes = TRUE) {
+  layer(
+    data = data,
+    mapping = mapping,
+    stat = StatBag,
+    geom = GeomBag,
+    position = position,
+    show.legend = show.legend,
+    inherit.aes = inherit.aes,
+    params = list(
+      na.rm = na.rm,
+      alpha = alpha,
+      prop = prop,
+      ...
+    )
+  )
+}
+
+#' @rdname ggplot2-ggproto
+#' @format NULL
+#' @usage NULL
+#' @export
+GeomBag <- ggproto("GeomBag", Geom,
+                   draw_group = function(data, panel_scales, coord) {
+                     n <- nrow(data)
+                     if (n == 1) return(zeroGrob())
+
+                     munched <- coord_munch(coord, data, panel_scales)
+                     # Sort by group to make sure that colors, fill, etc. come in same order
+                     munched <- munched[order(munched$group), ]
+
+                     # For gpar(), there is one entry per polygon (not one entry per point).
+                     # We'll pull the first value from each group, and assume all these values
+                     # are the same within each group.
+                     first_idx <- !duplicated(munched$group)
+                     first_rows <- munched[first_idx, ]
+
+                     ggplot2:::ggname("geom_bag",
+                                      grid:::polygonGrob(munched$x, munched$y, default.units = "native",
+                                                         id = munched$group,
+                                                         gp = grid::gpar(
+                                                           col = first_rows$colour,
+                                                           fill = alpha(first_rows$fill, first_rows$alpha),
+                                                           lwd = first_rows$size * .pt,
+                                                           lty = first_rows$linetype
+                                                         )
+                                      )
+                     )
+
+
+                   },
+
+                   default_aes = aes(colour = "NA", fill = "grey20", size = 0.5, linetype = 1,
+                                     alpha = NA, prop = 0.5),
+
+                   handle_na = function(data, params) {
+                     data
+                   },
+
+                   required_aes = c("x", "y"),
+
+                   draw_key = draw_key_polygon
+)