如何更改图中点的颜色？ ggpubr 包

Question

我正在使用 ggpubr 包的 ggerorplot () 函数来创建下图。我的问题是，是否有任何方法可以在不改变代表均值和标准差的点的颜色的情况下改变点的颜色？观察图像：

我的代码：

# loading packages
library(ggpubr)

# Create data frame
GROUP <- c()
TEST <- c()
VALUE <- c()
for (i in 0:100) {
  gp <- c('Group1','Group2','Group1 and Group2')
  ts <- c('Test1','Test2') 
  GROUP <- append(GROUP, sample(gp, 1))
  TEST <- append(TEST, sample(ts, 1))
  VALUE <-  append(VALUE, sample(1:200, 1))
}
df <- data.frame(GROUP, TEST, VALUE)

# Seed
set.seed(123)

# Plot
ggerrorplot(df, x = "GROUP", y = "VALUE",
            desc_stat = "mean_sd",
            add = c("jitter"),
            color = "TEST", 
            palette = "jco",
            add.params = list(size = 0.2),
            order = c('Group1','Group2','Group1 and Group2')
            ) +
  labs(x = '', y = 'Values\n') +
  theme(legend.title = element_blank())

Answer 1

另一个可能的解决方法 - 使用 ggplot() 和 geom_linerange() 复制绘图，例如

library(ggpubr)
library(ggsci)
library(cowplot)

# Create data frame
GROUP <- c()
TEST <- c()
VALUE <- c()
for (i in 0:100) {
  gp <- c('Group1','Group2','Group1 and Group2')
  ts <- c('Test1','Test2') 
  GROUP <- append(GROUP, sample(gp, 1))
  TEST <- append(TEST, sample(ts, 1))
  VALUE <-  append(VALUE, sample(1:200, 1))
}
df <- data.frame(GROUP, TEST, VALUE)

# Seed
set.seed(123)

data_summary <- function(data, varname, groupnames){
  require(plyr)
  summary_func <- function(x, col){
    c(mean = mean(x[[col]], na.rm=TRUE),
      sd = sd(x[[col]], na.rm=TRUE))
  }
  data_sum<-ddply(data, groupnames, .fun=summary_func,
                  varname)
  data_sum <- rename(data_sum, c("mean" = varname))
  return(data_sum)
}

df2 <- data_summary(df, varname = "VALUE", groupnames = c("TEST", "GROUP"))

# Plot
p1 <- ggplot(df, aes(x = factor(GROUP, levels = c('Group1','Group2','Group1 and Group2')),
               y = VALUE, color = TEST)) +
  geom_jitter(shape = 21, fill = "black", stroke = 0,
              position = position_jitterdodge(jitter.width = 0.2)) +
  geom_linerange(data = df2, aes(ymin=VALUE-sd, ymax=VALUE+sd),
                position=position_dodge(width = .75)) +
  geom_point(data = df2, aes(y = VALUE), size = 3,
             position = position_dodge(width = 0.75)) +
  scale_color_jco() +
  labs(x = '', y = 'Values\n') +
  theme_classic(base_size = 14) +
  theme(legend.title = element_blank(),
        legend.position = "top")

p2 <- ggerrorplot(df, x = "GROUP", y = "VALUE",
                  desc_stat = "mean_sd",
                  add = c("jitter"),
                  color = "TEST", 
                  palette = "jco",
                  add.params = list(size = 0.2),
                  order = c('Group1','Group2','Group1 and Group2')
) +
  labs(x = '', y = 'Values\n') +
  theme(legend.title = element_blank())

cowplot::plot_grid(p1, p2, nrow = 1, ncol = 2, labels = "AUTO")

当您将它们并排绘制时，您会发现它们并不完全相同，但这仍然对您有用。

编辑

这种方法的一个优点是，如果您不希望所有的点都具有相同的颜色，但您确实希望它们与线条不同，则可以单独调整 'fill' 比例，例如

p1 <- ggplot(df, aes(x = factor(GROUP, levels = c('Group1','Group2','Group1 and Group2')),
               y = VALUE, color = TEST)) +
  geom_jitter(aes(fill = TEST), shape = 21, stroke = 0,
              position = position_jitterdodge(jitter.width = 0.2)) +
  geom_linerange(data = df2, aes(ymin=VALUE-sd, ymax=VALUE+sd),
                position=position_dodge(width = .75)) +
  geom_point(data = df2, aes(y = VALUE), size = 3,
             position = position_dodge(width = 0.75)) +
  scale_color_jco() +
  scale_fill_npg() +
  labs(x = '', y = 'Values\n') +
  theme_classic(base_size = 14) +
  theme(legend.title = element_blank(),
        legend.position = "top")

p2 <- ggerrorplot(df, x = "GROUP", y = "VALUE",
                  desc_stat = "mean_sd",
                  add = c("jitter"),
                  color = "TEST", 
                  palette = "jco",
                  add.params = list(size = 0.2),
                  order = c('Group1','Group2','Group1 and Group2')
) +
  labs(x = '', y = 'Values\n') +
  theme(legend.title = element_blank())

cowplot::plot_grid(p1, p2, nrow = 1, ncol = 2, labels = "AUTO")

Answer 2

你能通过简单地将 color 传递给 add.params 来实现吗？

# loading packages
library(ggpubr)
#> Loading required package: ggplot2

# Create data frame
GROUP <- c()
TEST <- c()
VALUE <- c()
for (i in 0:100) {
  gp <- c('Group1','Group2','Group1 and Group2')
  ts <- c('Test1','Test2') 
  GROUP <- append(GROUP, sample(gp, 1))
  TEST <- append(TEST, sample(ts, 1))
  VALUE <-  append(VALUE, sample(1:200, 1))
}
df <- data.frame(GROUP, TEST, VALUE)

# Seed
set.seed(123)

# Plot
ggerrorplot(df, x = "GROUP", y = "VALUE",
            desc_stat = "mean_sd",
            add = c("jitter"),
            color = "TEST", 
            palette = "jco",
            add.params = list(size = 0.2, color = "red"),
            order = c('Group1','Group2','Group1 and Group2')
            ) +
  labs(x = '', y = 'Values\n') +
  theme(legend.title = element_blank())

^{由 reprex package (v0.3.0)}

于 2021 年 3 月 10 日创建

如何更改图中点的颜色？ ggpubr 包

How to change the colors of the dots in the graph? ggpubr package

r

ggplot2

ggpubr

编辑