ggplot：重新缩放轴（对数）和切割轴

Question

我想在 R 中绘制一个像这样的非常简单的箱线图：

想要的图表

是一个log-link（Gamma分布：jh_conc是一个激素浓度变量）一个分类分组变量的连续因变量（jh_conc）的广义线性模型（组：type of bee）

我已有的脚本是：

> jh=read.csv("data_jh_titer.csv",header=T)
> jh
           group     jh_conc
1         Queens  6.38542714
2         Queens 11.22512563
3         Queens  7.74472362
4         Queens 11.56834171
5         Queens  3.74020100
6  Virgin Queens  0.06080402
7  Virgin Queens  0.12663317
8  Virgin Queens  0.08090452
9  Virgin Queens  0.04422111
10 Virgin Queens  0.14673367
11       Workers  0.03417085
12       Workers  0.02449749
13       Workers  0.02927136
14       Workers  0.01648241
15       Workers  0.02150754

fit1=glm(jh_conc~group,family=Gamma(link=log), data=jh) 

ggplot(fit, aes(group, jh_conc))+
      geom_boxplot(aes(fill=group))+
      coord_trans(y="log")

结果图如下所示：

我的问题是：我可以使用什么（geom）扩展来拆分 y 轴并重新缩放它们？另外，我如何添加黑色圆圈（平均值；按对数刻度计算然后反向转换为原始刻度）水平线，它们是基于对对数转换数据执行的事后测试的显着性水平：**：p<0.01 , *** :p< 0.001?

Answer 1

您无法在 ggplot2 中创建一个破损的数字轴，主要是因为它在视觉上扭曲了所表示的 data/differences 并被认为具有误导性。

但是，您可以使用 scale_log10() + annotation_logticks() 来帮助压缩各种值的数据或更好地显示异方差数据。您还可以使用 annotate 构建您的 p-value 代表星和条。

您还可以使用它的命名属性轻松地从模型中获取信息，这里我们关心 fit$coef:

# make a zero intercept version for easy plotting
fit2 <- glm(jh_conc ~ 0 + group, family = Gamma(link = log), data = jh)
# extract relevant group means and use exp() to scale back
means <- data.frame(group = gsub("group", "",names(fit2$coef)), means = exp(fit2$coef))

ggplot(fit, aes(group, jh_conc)) +
    geom_boxplot(aes(fill=group)) +
    # plot the circles from the model extraction (means)
    geom_point(data = means, aes(y = means),size = 4, shape = 21, color = "black", fill = NA) +
    # use this instead of coord_trans
    scale_y_log10() + annotation_logticks(sides = "l") +
    # use annotate "segment" to draw the horizontal lines
    annotate("segment", x = 1, xend = 2, y = 15, yend = 15) +
    # use annotate "text" to add your pvalue *'s
    annotate("text", x = 1.5, y = 15.5, label = "**", size = 4) +
    annotate("segment", x = 1, xend = 3, y = 20, yend = 20) +
    annotate("text", x = 2, y = 20.5, label = "***", size = 4) +
    annotate("segment", x = 2, xend = 3, y = .2, yend = .2) +
    annotate("text", x = 2.5, y = .25, label = "**", size = 4)

ggplot：重新缩放轴（对数）和切割轴

ggplot: rescale axis (log) and cut axis

axis

r

ggplot2

boxplot