1 点图

1.1 geom_dotplot()

Code
library(tidyverse)
library(ggpubr)
ggplot(mtcars,aes(mpg))+
    geom_dotplot()
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.

Code
# 将数值型变量转换为因子
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
head(ToothGrowth)
#>    len supp dose
#> 1  4.2   VC  0.5
#> 2 11.5   VC  0.5
#> 3  7.3   VC  0.5
#> 4  5.8   VC  0.5
#> 5  6.4   VC  0.5
#> 6 10.0   VC  0.5
library(ggplot2)
# 基础点图
p1 <- ggplot(ToothGrowth, aes(x=dose, y=len)) + 
  geom_dotplot(binaxis='y', stackdir='center')
# 更改点尺寸和堆叠率
p2 <- ggplot(ToothGrowth, aes(x=dose, y=len)) + 
  geom_dotplot(binaxis='y', stackdir='center',
               stackratio=1.5, dotsize=1.2)
# 旋转
p3 <- p1 + coord_flip()
# 选择展示数据
p4 <- p1 + scale_x_discrete(limits=c("0.5", "2"))
ggarrange(p1,p2,p3,p4,nrow = 1)
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`stat_bindot()`).

Code
# 在点图上添加摘要统计信息 stat_summary()
# 添加平均值和中位数
p5 <- p1 + stat_summary(fun.y=mean, geom="point", shape=18,
                 size=3, color="red")
#> Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
#> ℹ Please use the `fun` argument instead.

# p6<- p1 + stat_summary(fun.y=median, geom="point", shape=18,
#                  size=3, color="red")

1.2 ggdotplot()

Code
Code

f6d <-
    read_excel("data/01source.xlsx", sheet = "Fig.6", range = "D2:E18")
f6d |> pivot_longer(
    cols = everything(),
    names_to = "status",
    values_to = "Ratio",
) |> 
    tidyr::drop_na() ->f6d
Code
ggdotplot(f6d,
          x="status",
          y="Ratio",
          add =c("mean_sd"),
          color = "status",
          fill = "status",
          error.plot = "errorbar",
)+
    geom_signif(
        comparisons = list(c("relapse","non-relapse")),
    )+
    
    stat_summary(
        fun.data = "mean_sd",geom = "pointrange",width=.3
    )+
    ggplot2::annotate(
        geom="segment",
        x=0.9,
        xend=1.1,
        y=2.42019873,#均值
    )+
    ggplot2::annotate(
        geom="segment",
        x=1.9,
        xend=2.1,
        y=0.789463173,#均值
    )
#> Warning in stat_summary(fun.data = "mean_sd", geom = "pointrange", width =
#> 0.3): Ignoring unknown parameters: `width`
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.

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