将自定义图像添加到geom_polygon中填充ggplot [英] Adding custom image to geom_polygon fill in ggplot
问题描述
学生问我是否可以使用R重新创建一个类似于下图的阴谋：
.stack.imgur.com / j0074.pngalt =这是来自我们可以轻松调整大小而不会对代码进行更改。
< a href =https://i.stack.imgur.com/poDEb.png =noreferrer>
当然，你应该记住你的机器的性能，并且可能不会选择20MP图片来绘制您的 ggplot =）
I was asked by a student if it was possible to recreate a plot similar to the one below using R:
This is from this paper....
This sort of stuff isn't my specialty, but using the following code I was able to create 95% CI ellipses and to plot them with geom_polygon(). I filled the images with images I grabbed from the phylopic library using the rphylopic package.
#example data/ellipses
set.seed(101)
n <- 1000
x1 <- rnorm(n, mean=2)
y1 <- 1.75 + 0.4*x1 + rnorm(n)
df <- data.frame(x=x1, y=y1, group="A")
x2 <- rnorm(n, mean=8)
y2 <- 0.7*x2 + 2 + rnorm(n)
df <- rbind(df, data.frame(x=x2, y=y2, group="B"))
x3 <- rnorm(n, mean=6)
y3 <- x3 - 5 - rnorm(n)
df <- rbind(df, data.frame(x=x3, y=y3, group="C"))
#calculating ellipses
library(ellipse)
df_ell <- data.frame()
for(g in levels(df$group)){
df_ell <- rbind(df_ell, cbind(as.data.frame(with(df[df$group==g,], ellipse(cor(x, y),
scale=c(sd(x),sd(y)),
centre=c(mean(x),mean(y))))),group=g))
}
#drawing
library(ggplot2)
p <- ggplot(data=df, aes(x=x, y=y,colour=group)) +
#geom_point(size=1.5, alpha=.6) +
geom_polygon(data=df_ell, aes(x=x, y=y,colour=group, fill=group), alpha=0.1, size=1, linetype=1)
### get center points of ellipses
library(dplyr)
ell_center <- df_ell %>% group_by(group) %>% summarise(x=mean(x), y=mean(y))
### animal images
library(rphylopic)
lion <- get_image("e2015ba3-4f7e-4950-9bde-005e8678d77b", size = "512")[[1]]
mouse <- get_image("6b2b98f6-f879-445f-9ac2-2c2563157025", size="512")[[1]]
bug <- get_image("136edfe2-2731-4acd-9a05-907262dd1311", size="512")[[1]]
### overlay images on center points
p + add_phylopic(lion, alpha=0.9, x=ell_center[[1,2]], y=ell_center[[1,3]], ysize=2, color="firebrick1") +
add_phylopic(mouse, alpha=1, x=ell_center[[2,2]], y=ell_center[[2,3]], ysize=2, color="darkgreen") +
add_phylopic(bug, alpha=0.9, x=ell_center[[3,2]], y=ell_center[[3,3]], ysize=2, color="mediumblue") +
theme_bw()
Which gives the following:
This is ok, but what I'd really like to do is to add an image directly to the 'fill' command of geom_polygon. Is this possible ?
We can not set pattern fill for ggplot, but we can make a quite simple workaround with the help of geom_tile. Reproducing your initial data:
#example data/ellipses
set.seed(101)
n <- 1000
x1 <- rnorm(n, mean=2)
y1 <- 1.75 + 0.4*x1 + rnorm(n)
df <- data.frame(x=x1, y=y1, group="A")
x2 <- rnorm(n, mean=8)
y2 <- 0.7*x2 + 2 + rnorm(n)
df <- rbind(df, data.frame(x=x2, y=y2, group="B"))
x3 <- rnorm(n, mean=6)
y3 <- x3 - 5 - rnorm(n)
df <- rbind(df, data.frame(x=x3, y=y3, group="C"))
#calculating ellipses
library(ellipse)
df_ell <- data.frame()
for(g in levels(df$group)){
df_ell <-
rbind(df_ell, cbind(as.data.frame(
with(df[df$group==g,], ellipse(cor(x, y), scale=c(sd(x),sd(y)),
centre=c(mean(x),mean(y))))),group=g))
}
The key feature I want to show is converting a raster image into data.frame with columns X, Y, color so we can later plot it with geom_tile
require("dplyr")
require("tidyr")
require("ggplot2")
require("png")
# getting sample pictures
download.file("http://content.mycutegraphics.com/graphics/alligator/alligator-reading-a-book.png", "alligator.png", mode = "wb")
download.file("http://content.mycutegraphics.com/graphics/animal/elephant-and-bird.png", "elephant.png", mode = "wb")
download.file("http://content.mycutegraphics.com/graphics/turtle/girl-turtle.png", "turtle.png", mode = "wb")
pic_allig <- readPNG("alligator.png")
pic_eleph <- readPNG("elephant.png")
pic_turtl <- readPNG("turtle.png")
# converting raster image to plottable data.frame
ggplot_rasterdf <- function(color_matrix, bottom = 0, top = 1, left = 0, right = 1) {
require("dplyr")
require("tidyr")
if (dim(color_matrix)[3] > 3) hasalpha <- T else hasalpha <- F
outMatrix <- matrix("#00000000", nrow = dim(color_matrix)[1], ncol = dim(color_matrix)[2])
for (i in 1:dim(color_matrix)[1])
for (j in 1:dim(color_matrix)[2])
outMatrix[i, j] <- rgb(color_matrix[i,j,1], color_matrix[i,j,2], color_matrix[i,j,3], ifelse(hasalpha, color_matrix[i,j,4], 1))
colnames(outMatrix) <- seq(1, ncol(outMatrix))
rownames(outMatrix) <- seq(1, nrow(outMatrix))
as.data.frame(outMatrix) %>% mutate(Y = nrow(outMatrix):1) %>% gather(X, color, -Y) %>%
mutate(X = left + as.integer(as.character(X))*(right-left)/ncol(outMatrix), Y = bottom + Y*(top-bottom)/nrow(outMatrix))
}
Converting images:
# preparing image data
pic_allig_dat <-
ggplot_rasterdf(pic_allig,
left = min(df_ell[df_ell$group == "A",]$x),
right = max(df_ell[df_ell$group == "A",]$x),
bottom = min(df_ell[df_ell$group == "A",]$y),
top = max(df_ell[df_ell$group == "A",]$y) )
pic_eleph_dat <-
ggplot_rasterdf(pic_eleph, left = min(df_ell[df_ell$group == "B",]$x),
right = max(df_ell[df_ell$group == "B",]$x),
bottom = min(df_ell[df_ell$group == "B",]$y),
top = max(df_ell[df_ell$group == "B",]$y) )
pic_turtl_dat <-
ggplot_rasterdf(pic_turtl, left = min(df_ell[df_ell$group == "C",]$x),
right = max(df_ell[df_ell$group == "C",]$x),
bottom = min(df_ell[df_ell$group == "C",]$y),
top = max(df_ell[df_ell$group == "C",]$y) )
As far as I got, author wants to plot images only inside ellipses, not in their original rectangular shape. We can achieve it with the help of point.in.polygon function from package sp.
# filter image-data.frames keeping only rows inside ellipses
require("sp")
gr_A_df <-
pic_allig_dat[point.in.polygon(pic_allig_dat$X, pic_allig_dat$Y,
df_ell[df_ell$group == "A",]$x,
df_ell[df_ell$group == "A",]$y ) %>% as.logical,]
gr_B_df <-
pic_eleph_dat[point.in.polygon(pic_eleph_dat$X, pic_eleph_dat$Y,
df_ell[df_ell$group == "B",]$x,
df_ell[df_ell$group == "B",]$y ) %>% as.logical,]
gr_C_df <-
pic_turtl_dat[point.in.polygon(pic_turtl_dat$X, pic_turtl_dat$Y,
df_ell[df_ell$group == "C",]$x,
df_ell[df_ell$group == "C",]$y ) %>% as.logical,]
And finally...
#drawing
p <- ggplot(data=df) +
geom_polygon(data=df_ell, aes(x=x, y=y,colour=group, fill=group), alpha=0.1, size=1, linetype=1)
p + geom_tile(data = gr_A_df, aes(x = X, y = Y), fill = gr_A_df$color) +
geom_tile(data = gr_B_df, aes(x = X, y = Y), fill = gr_B_df$color) +
geom_tile(data = gr_C_df, aes(x = X, y = Y), fill = gr_C_df$color) + theme_bw()
We can easily resize the plot without making changes to the code.
And, of course, you should keep in mind performance capabilities of your machine, and, probably, not choose 20MP pictures for plotting inside your ggplot =)
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