ggplot：使用包 RColorBrewer 填充箱线图 + 在 R 的 Cowplot 包中使用 plot_grid() 绘制箱线图

Question

概览

我有一个名为 'ANOVA.Dataframe.1' 和 'ANOVA.Dataframe.2' 的两个数据框（见下文）。

对于这个项目，我有两个目标：

(1) 使用包 RColorBrewer;

填充箱线图

(2) 使用包 Cowplot

绘制箱线图

问题

首先，我生成了两个 objects，名为 New.filled.Boxplot。obs1.Canopy.Urban 和 New.filled.Boxplot.obs2.Canopy.Urban，我添加了函数 （即函数 1 或函数 2 - 请参阅下面的 R-code）通过以下 scale_fill_brewer(palette="Dark2") 包中的 scale_fill_brewer(palette="Dark2") 函数生成箱线图 example 以产生所需的结果。但是，我的代码不起作用 （见下图）。
当我使用 plot_grid() 在 Cowplot 包 中绘制箱线图时，定位标签标题（即 A：观察期 1 或 B：观察期 2 - 见下图）覆盖两个箱线图（见下图）。有没有一种方法可以操纵情节 window 中的绘图 space，使箱线图稍微小一些，而标签标题位于每个箱线图上方？

如果有人能提供帮助，我将不胜感激。

R-Code

library(tidyverse)
library(wrapr)
library(RColorBrewer)
library(dplyr)

# Open Colour Brewer Paletter Options
display.brewer.all()


## Function 1 to produce the boxplots for Dataframe 1

Boxplot.obs1.Canopy.Urban<-ANOVA.Dataframe.1 %.>%
                                   ggplot(data = ., aes(
                                   x = Urbanisation_index,
                                   y = Canopy_Index,
                                   group = Urbanisation_index,
                                   )) +
                                   stat_boxplot(
                                   geom = 'errorbar',
                                   width = .25
                                   ) +
                                   geom_boxplot(notch=T) +
                                   geom_line(
                                   data = group_by(., Urbanisation_index) %>%
                                   summarise(
                                   bot = min(Canopy_Index),
                                   top = max(Canopy_Index)
                                    ) %>%
                                   gather(pos, val, bot:top) %>% 
                                   select(
                                   x = Urbanisation_index,
                                   y = val
                                   ) %>%
                                   mutate(gr = row_number()) %>%
                                   bind_rows(
                                   tibble(
                                   x = 0,
                                   y = max(.$y) * 1.15,
                                   gr = 1:8
                                   )
                                   ),
                                  aes(
                                  x = x,
                                  y = y,
                                  group = gr
                                  )) +
                                  theme_light() +
                                  theme(panel.grid = element_blank()) +
                                  coord_cartesian(
                                  xlim = c(min(.$Urbanisation_index) - .5, max(.$Urbanisation_index) + .5),
                                  ylim = c(min(.$Canopy_Index) * .95, max(.$Canopy_Index) * 1.05)
                                   ) +
                                 ylab('Company Index (%)') +
                                 xlab('Urbanisation Index')

 ## Change the colours of the boxplot
New.filled.Boxplot.obs1.Canopy.Urban <- Boxplot.obs1.Canopy.Urban + scale_fill_brewer(palette="Dark2")

## Function 2 to produce the boxplots for Dataframe 2
Boxplot.obs2.Canopy.Urban<-ANOVA.Dataframe.2 %.>%
                                   ggplot(data = ., aes(
                                   x = Urbanisation_index,
                                   y = Canopy_Index,
                                   group = Urbanisation_index,
                                   )) +
                                   stat_boxplot(
                                   geom = 'errorbar',
                                   width = .25
                                   ) +
                                   geom_boxplot(notch=T) +
                                   geom_line(
                                   data = group_by(., Urbanisation_index) %>%
                                   summarise(
                                   bot = min(Canopy_Index),
                                   top = max(Canopy_Index)
                                    ) %>%
                                   gather(pos, val, bot:top) %>% 
                                   select(
                                   x = Urbanisation_index,
                                   y = val
                                   ) %>%
                                   mutate(gr = row_number()) %>%
                                   bind_rows(
                                   tibble(
                                   x = 0,
                                   y = max(.$y) * 1.15,
                                   gr = 1:8
                                   )
                                   ),
                                  aes(
                                  x = x,
                                  y = y,
                                  group = gr
                                  )) +
                                  theme_light() +
                                  theme(panel.grid = element_blank()) +
                                  coord_cartesian(
                                  xlim = c(min(.$Urbanisation_index) - .5, max(.$Urbanisation_index) + .5),
                                  ylim = c(min(.$Canopy_Index) * .95, max(.$Canopy_Index) * 1.05)
                                   ) +
                                 ylab('Company Index (%)') +
                                 xlab('Urbanisation Index')


## Change the colours of the boxplot

 New.filled.Boxplot.obs2.Canopy.Urban<- Boxplot.obs2.Canopy.Urban + scale_fill_brewer(palette="Dark2")

library(cowplot)

## Open New plot window
dev.new()

Combined_boxplot_Obs<-plot_grid(New.filled.Boxplot.obs1.Canopy.Urban, 
                                New.filled.Boxplot.obs2.Canopy.Urban, 
                                labels=c("A: Observation Period 1",
                                         "B: Observation Period 2"),
                                label_fontface="bold",
                                label_fontfamily="Times New Roman",
                                label_size=12,
                                align="v",
                                ncol=2, nrow=1)

Combined_boxplot_Obs

这个 R-code 产生了这些图：

数据框1

structure(list(Urbanisation_index = c(2, 2, 4, 4, 3, 3, 4, 4, 
4, 2, 4, 3, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 
2, 2, 2, 4, 4, 3, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 
4, 4, 4, 4), Canopy_Index = c(65, 75, 55, 85, 85, 85, 95, 85, 
85, 45, 65, 75, 75, 65, 35, 75, 65, 85, 65, 95, 75, 75, 75, 65, 
75, 65, 75, 95, 95, 85, 85, 85, 75, 75, 65, 85, 75, 65, 55, 95, 
95, 95, 95, 45, 55, 35, 55, 65, 95, 95, 45, 65, 45, 55)), row.names = c(NA, 
-54L), class = "data.frame")

数据帧 2

structure(list(Urbanisation_index = c(2, 2, 4, 4, 3, 3, 4, 4, 
4, 3, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 
2, 2, 2, 4, 4, 3, 2, 2, 2, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4
), Canopy_Index = c(5, 45, 5, 5, 5, 5, 45, 45, 55, 15, 35, 45, 
5, 5, 5, 5, 5, 5, 35, 15, 15, 25, 25, 5, 5, 5, 5, 5, 5, 15, 25, 
15, 35, 25, 45, 5, 25, 5, 5, 5, 5, 55, 55, 15, 5, 25, 15, 15, 
15, 15)), row.names = c(NA, -50L), class = "data.frame")

Answer 1

scale_fill_brewer(palette = "Dark2") 在您的示例中不起作用，因为您没有提供 fill-美学。您需要将其添加到您的箱线图中。
plot_grid 中的标签应该是单个字母（或至少是短字母）以供在标题中参考。为了您的目的，我建议在原始情节中使用标题。
您的代码很难阅读，您可以减少使用的包的数量。我还缩短了名称，因为它们在这里并不那么重要，并且使一切都更加冗长。
我不会在 ggplot 调用中计算特殊统计数据，而是在单独的 data.frame 调用之前计算。

套餐

library(tidyverse)
library(cowplot)

第一个箱线图

# Calculate special positions for lines first
mydf.1.lines <- mydf.1 %>% 
  group_by(Urbanisation) %>%
  summarise(bot = min(Canopy), top = max(Canopy)) %>%
  gather(pos, val, bot:top) %>% 
  select(x = Urbanisation, y = val) %>%
  mutate(gr = row_number()) %>%
  bind_rows(tibble(x = 0, y = max(.$y) * 1.15, gr = 1:8))

# Calculate plot limits 
xlimits.1 <- with(mydf.1, c(min(Urbanisation) - .5, max(Urbanisation) + .5))
ylimits.1 <- with(mydf.1, c(min(Canopy) * .95, max(Canopy) * 1.05))

Boxplot.1 <- 
  ggplot(mydf.1, aes(Urbanisation, Canopy, group = Urbanisation)) +
  stat_boxplot(geom = 'errorbar', width = .25) +
  # Add a fill aesthetics in the geom_boxplot - call:
  geom_boxplot(aes(fill = factor(Urbanisation)), notch = TRUE) +
  geom_line(data = mydf.1.lines, 
            aes(x, y, group = gr)) +
  theme_light() +
  theme(panel.grid = element_blank()) +
  coord_cartesian(xlim = xlimits.1, ylim = ylimits.1) +
  ylab('Company Index (%)') +
  xlab('Urbanisation Index')

New.filled.Boxplot.1 <- Boxplot.1 + scale_fill_brewer(palette = "Dark2")

第二个箱线图
类似于第一个：

mydf.2.lines <- mydf.2 %>% 
  group_by(Urbanisation) %>%
  summarise(bot = min(Canopy), top = max(Canopy)) %>%
  gather(pos, val, bot:top) %>% 
  select(x = Urbanisation, y = val) %>%
  mutate(gr = row_number()) %>%
  bind_rows(tibble(x = 0, y = max(.$y) * 1.15, gr = 1:8))

xlimits.2 <- with(mydf.2, c(min(Urbanisation) - .5, max(Urbanisation) + .5))
ylimits.2 <- with(mydf.2, c(min(Canopy) * .95, max(Canopy) * 1.05))

Boxplot.2 <- 
  ggplot(mydf.2, aes(Urbanisation, Canopy, group = Urbanisation)) +
  stat_boxplot(geom = 'errorbar', width = .25) +
  geom_boxplot(aes(fill = factor(Urbanisation)), notch = TRUE) +
  geom_line(data = mydf.2.lines, 
            aes(x, y, group = gr)) +
  theme_light() +
  theme(panel.grid = element_blank()) +
  coord_cartesian(xlim = xlimits.2, ylim = ylimits.2) +
  ylab('Company Index (%)') +
  xlab('Urbanisation Index')

New.filled.Boxplot.2 <- Boxplot.2 + scale_fill_brewer(palette = "Dark2")

合并地块

plot_grid(New.filled.Boxplot.1 + ggtitle("A: Observation Period 1"),
          New.filled.Boxplot.2 + ggtitle("B: Observation Period 2"), 
          align = "v",
          ncol = 2,
          nrow = 1)

或者使用正确的标题规范和 hjust（感谢 Claus Wilke）：

plot_grid(New.filled.Boxplot.1 + ggtitle(""),
          New.filled.Boxplot.2 + ggtitle(""), 
          align = "v",
          labels = c("A: Observation Period 1", "B: Observation Period 2"),
          hjust = 0, 
          label_x = 0.01,
          ncol = 2,
          nrow = 1)

图外的箱线图
这里的问题是槽口在铰链外面。如果您为第二个情节（或两者）设置 notch = FALSE ，那没问题。或者，您也可以按照您已经建议的那样操纵 ylimits 。函数 with 仅指定 data.frame (mydf.2)，其中可以找到以下列。因此调用

ylimits.2 <- with(mydf.2, c(min(Canopy) * .95, max(Canopy) * 1.05))

等同于

ylimits.2 <- c(min(mydf.2$Canopy) * .95, max(mydf.2$Canopy) * 1.05)

你可以指定

ylimits.2 <- c(-20, max(mydf.2$Canopy) * 1.05)

这会将下限设置为 -20，将上限设置为第二个数据帧中 Canopy 索引最大值的 1.05 倍。

数据

mydf.1 <- 
  structure(list(Urbanisation = c(2, 2, 4, 4, 3, 3, 4, 4, 4, 2, 4, 3, 4, 4, 1, 
                                  1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 
                                  2, 2, 4, 4, 3, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 
                                  2, 1, 4, 4, 4, 4, 4, 4, 4), 
                 Canopy = c(65, 75, 55, 85, 85, 85, 95, 85, 85, 45, 65, 75, 75, 
                            65, 35, 75, 65, 85, 65, 95, 75, 75, 75, 65, 75, 65, 
                            75, 95, 95, 85, 85, 85, 75, 75, 65, 85, 75, 65, 55, 
                            95, 95, 95, 95, 45, 55, 35, 55, 65, 95, 95, 45, 65, 
                            45, 55)), 
            row.names = c(NA, -54L), class = "data.frame")

mydf.2 <- 
  structure(list(Urbanisation = c(2, 2, 4, 4, 3, 3, 4, 4, 4, 3, 4, 4, 4, 4, 1, 
                                  1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 
                                  2, 2, 4, 4, 3, 2, 2, 2, 2, 2, 2, 1, 1, 4, 4, 
                                  4, 4, 4, 4, 4), 
                 Canopy = c(5, 45, 5, 5, 5, 5, 45, 45, 55, 15, 35, 45, 5, 5, 5, 
                            5, 5, 5, 35, 15, 15, 25, 25, 5, 5, 5, 5, 5, 5, 15, 
                            25, 15, 35, 25, 45, 5, 25, 5, 5, 5, 5, 55, 55, 15, 
                            5, 25, 15, 15, 15, 15)), 
            row.names = c(NA, -50L), class = "data.frame")

ggplot：使用包 RColorBrewer 填充箱线图 + 在 R 的 Cowplot 包中使用 plot_grid() 绘制箱线图

ggplot: Fill Boxplots Using the Package RColorBrewer + Plot Boxplots Using plot_grid() in the Cowplot Package in R

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