使用`jitterdodge`时对齐ggplot中的点和误差线

Question

下面的可再现数据包含每个季节（夏季和冬季）的每个动物（猫和狗）的50个观测值，其中包含两个协变量（cov1和cov2）及其各自的误差估计（SE）。

library(ggplot2); library(dplyr); library(tidyr)
set.seed(123)
dat <- data.frame(Season = rep(c("Summer", "Winter"), each = 100),
                  Species = rep(c("Dog", "Cat", "Dog", "Cat"), each = 50),
                  cov1 = sample(1:100, 200, replace = TRUE),
                  cov1SE = rnorm(200),
                  cov2 = sample(1:100, 200, replace = TRUE),
                  cov2SE = rnorm(200))

head(dat)
  Season Species cov1      cov1SE cov2      cov2SE
1 Summer     Dog   29 -0.71040656   24 -0.07355602
2 Summer     Dog   79  0.25688371   69 -1.16865142
3 Summer     Dog   41 -0.24669188   23 -0.63474826
4 Summer     Dog   89 -0.34754260   32 -0.02884155
5 Summer     Dog   95 -0.95161857   18  0.67069597
6 Summer     Dog    5 -0.04502772   81 -1.65054654

下面我将数据收集为ggplot的长格式

EstLong <- dat %>% gather(Cov, Estimate, c(cov1, cov2))
SE <- dat %>% gather(Cov, SE, c(cov1SE, cov2SE))
datLong <- EstLong[ , c(1,2,5,6)]
datLong$SE <- SE[ , 6]

head(datLong)
  Season Species  Cov Estimate          SE
1 Summer     Dog cov1       29 -0.71040656
2 Summer     Dog cov1       79  0.25688371
3 Summer     Dog cov1       41 -0.24669188
4 Summer     Dog cov1       89 -0.34754260
5 Summer     Dog cov1       95 -0.95161857
6 Summer     Dog cov1        5 -0.04502772

我试图绘制所有点，并使用position_jitterdodge闪避和抖动点（如本SO post中所建议），但无法正确地将误差线与各个点对齐，如下所示。 position_dodge正确对齐点和误差线，但是需要jitter以减少沿x轴的重叠。 任何建议将不胜感激。

Jit <- position_jitterdodge(dodge.width=0.4)

ggplot(datLong, aes(y = Estimate, x = Cov, color = Species)) +
  geom_point(position = Jit, size = 1) +
  geom_errorbar(aes(ymin = Estimate-SE, ymax = Estimate+SE), width = 0.2, position = Jit) +
  theme_bw() +
  facet_wrap(~ Season, ncol = 1, scales = "free") +
  scale_color_manual(values = c("blue", "red"))

Answer 1

您可以扩展position_dodge来为数据生成一个固定jitter ：

myjit <- ggproto("fixJitter", PositionDodge,
                 width = 0.3,
                 dodge.width = 0.1,
                 jit = NULL,
                 compute_panel =  function (self, data, params, scales) 
                 {

                   #Generate Jitter if not yet
                   if(is.null(self$jit) ) {
                    self$jit <-jitter(rep(0, nrow(data)), amount=self$dodge.width)
                   }

                   data <- ggproto_parent(PositionDodge, self)$compute_panel(data, params, scales)

                   data$x <- data$x + self$jit
                   #For proper error extensions
                   if("xmin" %in% colnames(data)) data$xmin <- data$xmin + self$jit
                   if("xmax" %in% colnames(data)) data$xmax <- data$xmax + self$jit
                   data
                 } )




ggplot(datLong, aes(y = Estimate, x = Cov, color = Species, group=Species)) +
  geom_point(position = myjit, size = 1) +
  geom_errorbar(aes(ymin = Estimate-SE, ymax = Estimate+SE), width = 0.2, position = myjit)+
  theme_bw() +
  facet_wrap(~ Season, ncol = 1, scales = "free") +
  scale_color_manual(values = c("blue", "red"))

请注意，您必须为每个图创建一个新的对象fixJitter 。

这是情节：