創建具有成對點和正確方向的拆分小提琴圖

使用ggplot2，我可以創建一個帶有重疊點的小提琴圖，并且可以使用 連接成對的點geom_line()。

library(datasets)
library(ggplot2)
library(dplyr)

iris_edit <- iris %>% group_by(Species) %>%
  mutate(paired = seq(1:length(Species))) %>%
  filter(Species %in% c("setosa","versicolor"))

ggplot(data = iris_edit,
       mapping = aes(x = Species, y = Sepal.Length, fill = Species))  
  geom_violin()  
  geom_line(mapping = aes(group = paired),
            position = position_dodge(0.1),
            alpha = 0.3)  
  geom_point(mapping = aes(fill = Species, group = paired),
             size = 1.5, shape = 21,
             position = position_dodge(0.1))  
  theme_classic()  
  theme(legend.position = "none",
        axis.text.x = element_text(size = 15),
        axis.title.y = element_text(size = 15),
        axis.title.x = element_blank(),
        axis.text.y = element_text(size = 10))

該see軟體包包括在geom_violindot()其組成點旁邊繪制對半小提琴圖的功能。我發現這個功能在繪制大量點時很有用，這樣小提琴就不會被遮擋。

library(see)

ggplot(data = iris_edit,
       mapping = aes(x = Species, y = Sepal.Length, fill = Species))  
  geom_violindot(dots_size = 0.8,
                 position_dots = position_dodge(0.1))  
  theme_classic()  
  theme(legend.position = "none",
        axis.text.x = element_text(size = 15),
        axis.title.y = element_text(size = 15),
        axis.title.x = element_blank(),
        axis.text.y = element_text(size = 10))

現在，我想添加geom_line()以geom_violindot()連接成對的點，如第一張圖片所示。理想情況下，我希望點在里面，小提琴在外面，這樣線條就不會與小提琴相交。geom_violindot()包括flip引數，它采用指定要翻轉的幾何圖形的數字向量。

ggplot(data = iris_edit,
       mapping = aes(x = Species, y = Sepal.Length, fill = Species))  
  geom_violindot(dots_size = 0.8,
                 position_dots = position_dodge(0.1),
                 flip = c(1))  
  geom_line(mapping = aes(group = paired),
            alpha = 0.3,
            position = position_dodge(0.1))  
  theme_classic()  
  theme(legend.position = "none",
        axis.text.x = element_text(size = 15),
        axis.title.y = element_text(size = 15),
        axis.title.x = element_blank(),
        axis.text.y = element_text(size = 10))

As you can see, invoking flip inverts the violin half, but not the corresponding points. The see documentation does not seem to address this.

Questions

1. How can you create a geom_violindot() plot with paired points, such that the points and the lines connecting them are "sandwiched" in between the violin halves? I suspect there is a solution that uses David Robinson's GeomFlatViolin function, though I haven't been able to figure it out.
2. In the last figure, note that the lines are askew relative to the points they connect. What position adjustment function should be supplied to the position_dots and position arguments so that the points and lines are properly aligned?

uj5u.com熱心網友回復：

不確定是否將 geom_violindot 與 see 包一起使用。但是您可以將 geom_half_violon 和 geom_half_dotplot 與 gghalves 包結合使用，并對資料進行子集化以指定方向：

library(gghalves)

 ggplot(data = iris_edit[iris_edit$Species == "setosa",],
           mapping = aes(x = Species, y = Sepal.Length, fill = Species))  
   geom_half_violin(side = "l")  
    geom_half_dotplot(stackdir = "up")  
    geom_half_violin(data = iris_edit[iris_edit$Species == "versicolor",],
                     aes(x = Species, y = Sepal.Length, fill = Species), side = "r") 
    geom_half_dotplot(data = iris_edit[iris_edit$Species == "versicolor",],
                      aes(x = Species, y = Sepal.Length, fill = Species),stackdir = "down")  
    geom_line(data = iris_edit, mapping = aes(group = paired),
              alpha = 0.3)

請注意，配對中的線不會正確對齊，因為點圖正在對每個觀察結果進行分箱，然后延長點線 - 配對線僅對應于 aes 中定義的 x 值，而不對應于線中點的位置.

uj5u.com熱心網友回復：

根據評論 - 這不是對您問題的直接回答，但我相信在使用“斜率圖”光學元件時您可能無法獲得最有說服力的可視化效果。這很快就會變得復雜（很多點/線重疊）并且資訊丟失了。

要顯示成對觀察（治療 1 與治療 2）之間的變化，您還可以（我認為：更好）使用散點圖。您可以顯示每個觀察結果，變化立即變得清晰。為了使它更直觀，您可以添加一行等式。

我認為您不需要顯示估計的分布（左圖），但是如果您想顯示這一點，您可以使用帶有 geom_density2d（右圖）的二維密度估計

library(tidyverse)
## patchwork only for demo purpose
library(patchwork)

iris_edit <- iris %>% group_by(Species) %>%
  ## use seq_along instead
  mutate(paired = seq_along(Species)) %>%
  filter(Species %in% c("setosa","versicolor")) %>%
## some more modificiations
  select(paired, Species, Sepal.Length) %>%
  pivot_wider(names_from = Species, values_from = Sepal.Length)

lims <- c(0, 10)

p1 <- 
  ggplot(data = iris_edit, aes(setosa, versicolor))  
  geom_abline(intercept = 0, slope = 1, lty = 2)  
  geom_point(alpha = .7, stroke = 0, size = 2)  
  cowplot::theme_minimal_grid()  
  coord_equal(xlim = lims, ylim = lims)  
  labs(x = "Treatment 1", y = "Treatment 2")

p2 <- 
  ggplot(data = iris_edit, aes(setosa, versicolor))  
  geom_abline(intercept = 0, slope = 1, lty = 2)  
  geom_density2d(color = "Grey")  
  geom_point(alpha = .7, stroke = 0, size = 2)  
  cowplot::theme_minimal_grid()  
  coord_equal(xlim = lims, ylim = lims)  
  labs(x = "Treatment 1", y = "Treatment 2")

p1  p2

^{由reprex 包(v2.0.1)于 2021 年 12 月 18 日創建}

標籤：r ggplot2 violin-plot

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