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如何在指数(log10)y轴上的方框图上方显示p值?

ggplot2 r

1

tassones · 技术社区 · 4 年前

我有一个包含三个组(组1、组2、组3)的数据帧。我想在中显示它们的平均值比较的p值 ggplot2 然而,我可以做到的是,这些值是堆叠在一起的,很难看到正在进行比较的内容。当我尝试使用 y_position() 函数,箱图折叠(我认为是因为y轴是log10),但p值不再堆叠在一起。如何防止箱线图塌陷,并保持p值的显示,以便您可以看到正在进行的比较?

示例数据

library(ggplot2)
library(dplyr)
library(ggsignif)

df <- data.frame(matrix(ncol = 2, nrow = 30))
colnames(df)[1:2] <- c("group", "value")
df$group <- rep(c("group1","group2","group3"), each = 10)
df[1:10,2] <- rexp(10, 1/10)
df[11:20,2] <- rexp(10, 1/100)
df[21:30,2] <- rexp(10, 1/900)

# Need to say what should be compared for p-value determination

my_comparisons <- list(c("group1", "group2"),
                       c("group1", "group3"),
                       c("group2", "group3"))

显示分布的方框图 value 然而,对于每个组,p值是彼此的上下,因此无法在组之间进行比较。

df %>%
  mutate(group = factor(group, levels = c("group3","group2","group1"))) %>%
  ggplot(aes(x = group, y = value)) +
  geom_signif(comparisons = my_comparisons,
              map_signif_level = function(x) paste("p =", scales::pvalue(x))) +
  scale_y_log10() +
  geom_boxplot(outlier.colour="white", outlier.fill = "white", outlier.shape = 1, outlier.size = 0) +
  geom_jitter(shape=1, position=position_jitter(0.2), color = "black", fill = "white", size = 2) +
  labs(x = "",
       y = "value") +
  theme_bw() +
  theme(axis.text.x = element_text(size = 16, color = "black"),
        axis.text.y = element_text(size = 16, color = "black"),
        axis.title = element_text(size = 16, color = "black"),
        axis.title.x = element_text(vjust = -0.5),
        panel.grid = element_blank(),
        panel.background = element_blank())

调整 y_position() p值应该显示在哪里,但这会折叠y轴。我在中尝试了几个值 y_position .

df %>%
  mutate(group = factor(group, levels = c("group3","group2","group1"))) %>%
  ggplot(aes(x = group, y = value)) +
  geom_signif(y_position = c(2000,1800,1600),
              comparisons = my_comparisons,
              map_signif_level = function(x) paste("p =", scales::pvalue(x))) +
  scale_y_log10() +
  geom_boxplot(outlier.colour="white", outlier.fill = "white", outlier.shape = 1, outlier.size = 0) +
  geom_jitter(shape=1, position=position_jitter(0.2), color = "black", fill = "white", size = 2) +
  labs(x = "",
       y = "value") +
  theme_bw() +
  theme(axis.text.x = element_text(size = 16, color = "black"),
        axis.text.y = element_text(size = 16, color = "black"),
        axis.title = element_text(size = 16, color = "black"),
        axis.title.x = element_text(vjust = -0.5),
        panel.grid = element_blank(),
        panel.background = element_blank())

1 回复 | 直到 4 年前

1

Allan Cameron 4 年前

由于某些原因,此参数会忽略轴变换。因此,您需要使用所需位置的log10值:


df %>%
  mutate(group = factor(group, levels = c("group3","group2","group1"))) %>%
  ggplot(aes(x = group, y = value)) +
  geom_signif(comparisons = my_comparisons,
              y_position = log10(c(5000, 10000, 25000)),
              map_signif_level = function(x) paste("p =", scales::pvalue(x))) +
  scale_y_log10() +
  geom_boxplot(outlier.colour="white", outlier.fill = "white", 
               -outlier.shape = 1, outlier.size = 0) +
  geom_jitter(shape=1, position=position_jitter(0.2), color = "black", 
              fill = "white", size = 2) +
  labs(x = "",
       y = "value") +
  theme_bw() +
  theme(axis.text.x = element_text(size = 16, color = "black"),
        axis.text.y = element_text(size = 16, color = "black"),
        axis.title = element_text(size = 16, color = "black"),
        axis.title.x = element_text(vjust = -0.5),
        panel.grid = element_blank(),
        panel.background = element_blank())