[英]Split violin plot with ggplot2
我想使用 ggplot 创建一个分离的小提琴密度图,就像 seaborn 文档这一页上的第四个例子一样。
这是一些数据:
set.seed(20160229)
my_data = data.frame(
y=c(rnorm(1000), rnorm(1000, 0.5), rnorm(1000, 1), rnorm(1000, 1.5)),
x=c(rep('a', 2000), rep('b', 2000)),
m=c(rep('i', 1000), rep('j', 2000), rep('i', 1000))
)
我可以像这样绘制闪避的小提琴:
library('ggplot2')
ggplot(my_data, aes(x, y, fill=m)) +
geom_violin()
但是很难直观地比较并排分布中不同点的宽度。 我没能在 ggplot 中找到任何分离小提琴的例子——这可能吗?
我找到了一个基本的 R 图形解决方案,但函数很长,我想突出显示分布模式,这些模式很容易添加为 ggplot 中的附加层,但如果我需要弄清楚如何编辑该函数,将很难做到。
或者,为了避免摆弄密度,您可以像这样扩展ggplot2
的GeomViolin :
GeomSplitViolin <- ggproto("GeomSplitViolin", GeomViolin,
draw_group = function(self, data, ..., draw_quantiles = NULL) {
data <- transform(data, xminv = x - violinwidth * (x - xmin), xmaxv = x + violinwidth * (xmax - x))
grp <- data[1, "group"]
newdata <- plyr::arrange(transform(data, x = if (grp %% 2 == 1) xminv else xmaxv), if (grp %% 2 == 1) y else -y)
newdata <- rbind(newdata[1, ], newdata, newdata[nrow(newdata), ], newdata[1, ])
newdata[c(1, nrow(newdata) - 1, nrow(newdata)), "x"] <- round(newdata[1, "x"])
if (length(draw_quantiles) > 0 & !scales::zero_range(range(data$y))) {
stopifnot(all(draw_quantiles >= 0), all(draw_quantiles <=
1))
quantiles <- ggplot2:::create_quantile_segment_frame(data, draw_quantiles)
aesthetics <- data[rep(1, nrow(quantiles)), setdiff(names(data), c("x", "y")), drop = FALSE]
aesthetics$alpha <- rep(1, nrow(quantiles))
both <- cbind(quantiles, aesthetics)
quantile_grob <- GeomPath$draw_panel(both, ...)
ggplot2:::ggname("geom_split_violin", grid::grobTree(GeomPolygon$draw_panel(newdata, ...), quantile_grob))
}
else {
ggplot2:::ggname("geom_split_violin", GeomPolygon$draw_panel(newdata, ...))
}
})
geom_split_violin <- function(mapping = NULL, data = NULL, stat = "ydensity", position = "identity", ...,
draw_quantiles = NULL, trim = TRUE, scale = "area", na.rm = FALSE,
show.legend = NA, inherit.aes = TRUE) {
layer(data = data, mapping = mapping, stat = stat, geom = GeomSplitViolin,
position = position, show.legend = show.legend, inherit.aes = inherit.aes,
params = list(trim = trim, scale = scale, draw_quantiles = draw_quantiles, na.rm = na.rm, ...))
}
像这样使用新的geom_split_violin
:
ggplot(my_data, aes(x, y, fill = m)) + geom_split_violin()
注意 :我认为jan-glx的答案要好得多,大多数人应该改用它。
您可以通过自己先计算密度,然后绘制多边形来实现。 大致请见下文。
library(dplyr)
pdat <- my_data %>%
group_by(x, m) %>%
do(data.frame(loc = density(.$y)$x,
dens = density(.$y)$y))
pdat$dens <- ifelse(pdat$m == 'i', pdat$dens * -1, pdat$dens)
pdat$dens <- ifelse(pdat$x == 'b', pdat$dens + 1, pdat$dens)
ggplot(pdat, aes(dens, loc, fill = m, group = interaction(m, x))) +
geom_polygon() +
scale_x_continuous(breaks = 0:1, labels = c('a', 'b')) +
ylab('density') +
theme_minimal() +
theme(axis.title.x = element_blank())
现在可以通过使用geom_split_violin function 的introdataviz package 来做到这一点,这使得创建这些图变得非常容易。 这是一个可重现的示例:
set.seed(20160229)
my_data = data.frame(
y=c(rnorm(1000), rnorm(1000, 0.5), rnorm(1000, 1), rnorm(1000, 1.5)),
x=c(rep('a', 2000), rep('b', 2000)),
m=c(rep('i', 1000), rep('j', 2000), rep('i', 1000))
)
library(ggplot2)
# devtools::install_github("psyteachr/introdataviz")
library(introdataviz)
ggplot(my_data, aes(x = x, y = y, fill = m)) +
geom_split_violin()
使用reprex v2.0.2创建于 2022-08-24
如您所见,它创建了一个分裂小提琴 plot。 如果您想了解更多信息和此 package 的教程,请查看上面的链接。
@jan-jlx 的解决方案很棒。 对于尾巴较细的密度,我想在小提琴的两半之间插入一点空间,以便更容易区分尾巴。 这是对@jan-jlx 的代码的轻微修改,借用了 gghalves 包中的 nudge 参数:
GeomSplitViolin <- ggplot2::ggproto(
"GeomSplitViolin",
ggplot2::GeomViolin,
draw_group = function(self,
data,
...,
nudge = 0,
draw_quantiles = NULL) {
data <- transform(data,
xminv = x - violinwidth * (x - xmin),
xmaxv = x + violinwidth * (xmax - x))
grp <- data[1, "group"]
newdata <- plyr::arrange(transform(data,
x = if (grp %% 2 == 1) xminv else xmaxv),
if (grp %% 2 == 1) y else -y)
newdata <- rbind(newdata[1, ],
newdata,
newdata[nrow(newdata), ],
newdata[1, ])
newdata[c(1, nrow(newdata)-1, nrow(newdata)), "x"] <- round(newdata[1, "x"])
newdata$x <- ifelse(newdata$group %% 2 == 1,
newdata$x - nudge,
newdata$x + nudge)
if (length(draw_quantiles) > 0 & !scales::zero_range(range(data$y))) {
stopifnot(all(draw_quantiles >= 0), all(draw_quantiles <= 1))
quantiles <- ggplot2:::create_quantile_segment_frame(data,
draw_quantiles)
aesthetics <- data[rep(1, nrow(quantiles)),
setdiff(names(data), c("x", "y")),
drop = FALSE]
aesthetics$alpha <- rep(1, nrow(quantiles))
both <- cbind(quantiles, aesthetics)
quantile_grob <- ggplot2::GeomPath$draw_panel(both, ...)
ggplot2:::ggname("geom_split_violin",
grid::grobTree(ggplot2::GeomPolygon$draw_panel(newdata, ...),
quantile_grob))
}
else {
ggplot2:::ggname("geom_split_violin",
ggplot2::GeomPolygon$draw_panel(newdata, ...))
}
}
)
geom_split_violin <- function(mapping = NULL,
data = NULL,
stat = "ydensity",
position = "identity",
nudge = 0,
...,
draw_quantiles = NULL,
trim = TRUE,
scale = "area",
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE) {
ggplot2::layer(data = data,
mapping = mapping,
stat = stat,
geom = GeomSplitViolin,
position = position,
show.legend = show.legend,
inherit.aes = inherit.aes,
params = list(trim = trim,
scale = scale,
nudge = nudge,
draw_quantiles = draw_quantiles,
na.rm = na.rm,
...))
}
这是我用geom_split_violin(nudge = 0.02)
得到的图。
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