凸面船体与ggbiplot

Question

根据下面的帮助，我尝试使用此脚本绘制PCA和Convex船体，但没有成功，任何想法我该如何解决？

library(ggbiplot)
library(plyr)

data <-read.csv("C:/Users/AAA.csv")
my.pca <- prcomp(data[,1:9] , scale. = TRUE)


find_hull <- function(my.pca) my.pca[chull(my.pca$x[,1], my.pca$x[,2]), ]
hulls <- ddply(my.pca , "Group", find_hull)

ggbiplot(my.pca, obs.scale = 1, var.scale = 1,groups = data$Group) + 
  scale_color_discrete(name = '') + geom_polygon(data=hulls, alpha=.2) + 
  theme_bw() + theme(legend.direction = 'horizontal', legend.position = 'top')

感谢。

以下脚本使用省略号绘制PCA（从https://github.com/vqv/ggbiplot略微修改后的示例为'opts'）已弃用）

library(ggbiplot)
data(wine)
wine.pca <- prcomp(wine, scale. = TRUE)
g <- ggbiplot(wine.pca, obs.scale = 1, var.scale = 1, 
              groups = wine.class, ellipse = TRUE, circle = TRUE)
g <- g + scale_color_discrete(name = '')
g <- g + theme(legend.direction = 'horizontal', legend.position = 'top')
print(g)

删除省略号很容易，但我试图用Convex船体替换它们没有任何成功，不知道怎么做？

由于

Answer 1

是的，我们可以为ggplot设计一个新的geom，然后将它与ggbiplot一起使用。这是一个新的geom，将做凸壳：

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
)

这里它与ggbiplot一起使用，我们将prop设置为1表示我们想要绘制一个包含所有点的多边形：

library(ggbiplot)
data(wine)
wine.pca <- prcomp(wine, scale. = TRUE)
g <- ggbiplot(wine.pca, obs.scale = 1, var.scale = 1, 
              groups = wine.class, ellipse = FALSE, circle = TRUE)
g <- g + scale_color_discrete(name = '')
g <- g + theme(legend.direction = 'horizontal', legend.position = 'top')
g + geom_bag(aes(group = wine.class, fill = wine.class), prop = 1) 

Answer 2

我们也可以使用ggbiplot和一个名为ggpubr的新pkg：

library(ggpubr)
library(ggbiplot)
data(wine)
wine.pca <- prcomp(wine, scale. = TRUE)

ggbiplot(
  wine.pca,
  obs.scale = 1,
  var.scale = 1,
  groups = wine.class,
  ellipse = FALSE,
  circle = TRUE
) + 
  stat_chull(aes(color = wine.class, 
                 fill = wine.class), 
             alpha = 0.1, 
             geom = "polygon") +
  scale_colour_brewer(palette = "Set1",
                      name = '',
                      guide = 'none') +
  scale_fill_brewer(palette = "Set1",
                      name = '')  +
  theme_minimal()

我使用scale_colour_brewer和scale_fill_brewer来控制船体和点的颜色，并抑制其中一个传说。

为了在多个图上保持相同的颜色，我认为将类别转换为有序因子并确保所有绘制数据集中的每个级别的因子都应该这样做。