如何改变图形中点的颜色？ggpubr包

Question

我正在使用ggpubr包的ggerrorplot ()函数来创建下面的图表。我的问题是，是否有任何方法可以改变点的颜色，而不改变代表均值和标准差的点的颜色？观察图像：

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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

另一种可能的解决方法是使用ggplot()和geom_linerange()复制绘图。

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")

当你把它们并排画在一起的时候，你会发现它们并不完全一样，但这对你来说还是可行的。

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编辑

这种方法的一个优点是，如果您不希望所有的点都是相同的颜色，则可以单独调整“填充”比例，但是您确实希望它们与线条不同。

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")

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