使用ggsignif优雅添加显著性标记详解

目录

• 引言
• PART1：安装
• PART2：函数部分参数详解
• PART3：示例——以ggplot2内置数据集mpg为例
• PART4：来点花的——何必一定是显著性标记？
• PART5：让图“躺”下来？

#从cran安装：
install.packages("ggsignif")
#从GitHub安装（最新版）：
install.packages("remotes")
remotes::install_github("const-ae/ggsignif")

?geom_signif

geom_signif(
  mapping = NULL,
  data = NULL,
  stat = "signif",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  comparisOns= NULL,
  test = "wilcox.test",
  test.args = NULL,
  annotatiOns= NULL,
  map_signif_level = FALSE,
  y_position = NULL,
  xmin = NULL,
  xmax = NULL,
  margin_top = 0.05,
  step_increase = 0,
  extend_line = 0,
  tip_length = 0.03,
  size = 0.5,
  textsize = 3.88,
  family = "",
  vjust = 0,
  parse = FALSE,
  manual = FALSE,
  orientation = NA,
  ...
)

· comparisons #指定比较对象，是一个由长度为2的向量组成的列表
· test #指定使用的检验方法，包括 wilcox.test 和 t.test
· annotations #指定注释的内容
· map_signif_level #布尔型变量，如果为TRUE，就用诸如***的形式来展示显著性差异
· y_position #指定标记在y轴方向上的坐标，是个数字向量
· xmin, xmax #指定标记在x轴方向上的位置，是个数字向量
· tip_length #指定标记小竖线的长度，是个数字向量
· size #指定标记尺寸，即线条的粗线
· textsize #指定标记中文字部分的大小
· family #指定标记中文字部分的字体
· vjust #指定标记部分中的文字与标记中的短横线之间的距离，负值在横线上方，正值在下方
· orientation #指定整个图的方向，一般不会修改，如果想让图“躺下”，就设置成为"y"

library(ggplot2)
head(mpg)

# A tibble: 6 x 11
  manufacturer model displ  year   cyl trans      drv     cty   hwy fl    class  
                          
1 audi         a4      1.8  1999     4 auto(l5)   f        18    29 p     compact
2 audi         a4      1.8  1999     4 manual(m5) f        21    29 p     compact
3 audi         a4      2    2008     4 manual(m6) f        20    31 p     compact
4 audi         a4      2    2008     4 auto(av)   f        21    30 p     compact
5 audi         a4      2.8  1999     6 auto(l5)   f        16    26 p     compact
6 audi         a4      2.8  1999     6 manual(m5) f        18    26 p     compact

library(ggsignif)

ggplot(data = mpg, aes(x = class, y = hwy)) + 
  geom_boxplot(aes(group = class, fill = class), size = 1) + #指定箱子线条宽度为1
  geom_signif(comparisOns= list(c("midsize", "minivan"), c("compact", "midsize")), #指定比较对象
              test = "t.test", #指定检验方法
              y_position = c(40, 47), #指定两个标记在y轴上的坐标，按照前面指定比较对象的顺序
              size = 1, #指定标记中线条的尺寸
              textsize = 5, #指定标记中文字部分的大小
              vjust = -0.3, #指定标记中文字部分与横线之间的距离
              tip_length = c(0.2, 0.45, 0.05, 0.05), #指定短竖线的长度
              map_signif_level = T) + 
  scale_y_continuous(limits = c(10, 55)) +
  theme(legend.position = "none",
        panel.background = element_rect(fill = NA),
        panel.border = element_rect(fill = NA, colour = "black", size = 1),
        axis.title = element_text(size = 15, face = "bold"),
        axis.text.x = element_text(size = 12, hjust = 1, angle = 45, color = "black"),
        axis.title.y = element_text(size = 12, color = "black"))

ggplot(data = mpg, aes(x = class, y = hwy)) + 
  geom_boxplot(aes(group = class, fill = class), size =1) +
  geom_signif(comparisOns= list(c("midsize", "minivan"), c("compact", "midsize")),
              annotatiOns= c("B", "A"), #差别在这儿
              y_position = c(40, 47),
              size = 1,
              textsize = 5,
              vjust = -0.3,
              tip_length = c(0.2, 0.45, 0.05, 0.05)) + 
  scale_y_continuous(limits = c(10, 55)) +
  theme(legend.position = "none",
        panel.background = element_rect(fill = NA),
        panel.border = element_rect(fill = NA, colour = "black", size = 1),
        axis.title = element_text(size = 15, face = "bold"),
        axis.text.x = element_text(size = 12, hjust = 1, angle = 45, color = "black"),
        axis.title.y = element_text(size = 12, color = "black"))

ggplot(data = mpg, aes(x = hwy, y = class)) +  #这里改了
  geom_boxplot(aes(group = class, fill = class), size =1, orientation = "y") +
  geom_signif(comparisOns= list(c("midsize", "minivan"), c("compact", "midsize")),
              test = "t.test",
              y_position = c(40, 47),
              size = 1,
              textsize = 5,
              vjust = -0.3,
              tip_length = c(0.2, 0.45, 0.05, 0.05),
              map_signif_level = T,
              orientation = "y") +  #这里改了
  scale_x_continuous(limits = c(10, 55)) + #这里改了
  theme(legend.position = "none",
        panel.background = element_rect(fill = NA),
        panel.border = element_rect(fill = NA, colour = "black", size = 1),
        axis.title = element_text(size = 15, face = "bold"),
        axis.text.x = element_text(size = 12, hjust = 1, angle = 45, color = "black"),
        axis.title.y = element_text(size = 12, color = "black"))

ggplot(data = mpg, aes(x = class, y = hwy)) + 
  geom_boxplot(aes(group = class, fill = class), size =1) +
  geom_signif(comparisOns= list(c("midsize", "minivan"), c("compact", "midsize")),
              test = "t.test",
              y_position = c(40, 47),
              size = 1,
              textsize = 5,
              vjust = -0.3,
              tip_length = c(0.2, 0.45, 0.05, 0.05),
              map_signif_level = T) + 
  scale_y_continuous(limits = c(10, 55)) +
  theme(legend.position = "none",
        panel.background = element_rect(fill = NA),
        panel.border = element_rect(fill = NA, colour = "black", size = 1),
        axis.title = element_text(size = 15, face = "bold"),
        axis.text.x = element_text(size = 12, hjust = 1, angle = 45, color = "black"),
        axis.title.y = element_text(size = 12, color = "black")) +
  coord_flip() #只改了这里