使用`jitterdodge`时对齐ggplot中的点和误差条 [英] align points and error bars in ggplot when using `jitterdodge`

问题描述

下面的可重现数据包含每个动物（猫和狗）对于两个协变量（cov1和cov2）和它们各自的误差估计（SE）的每个季节（夏季和冬季）的50个观测值。

  library（ggplot2）;库（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） 
季节种类cov1 cov1SE cov2 cov2SE 
 1夏日狗29 -0.71040656 24 -0.07355602 
 2夏日狗79 0.25688371 69 -1.16865142 
夏日狗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））$ b $ （SEV，SE，c（COV1SE，COV2SE））
 datLong <-EstLong [，c（1,2,5,6）] 
 datlong $ SE<  -  SE [，6] 
 
头（datlong）
赛季种类Cov估计SE 
 1夏季狗队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 来闪避和抖动的点（如

解决方案

您可以扩展 position_dodge 来生成一个修正抖动为数据：

  myjit < -  ggproto（fixJitter，PositionDodge，
 width = 0.3，
 dodge.width = 0.1，
 jit = NULL，
 compute_panel =函数（self，data，params，scale）
 {
 
 #Generate Jitter if if not尚未
 if（is.null（self $ jit））{
 self $ jit< -jitter（rep（0，nrow（data）），amount = self $ dodge.width）
} 
 
 data <-ggproto_parent（PositionDodge，self）$ compute_panel（数据，参数，比例）
 
 data $ x < -  data $ x + self $ jit 
＃为正确的错误扩展
 if（xmin％in％colnames（ （data））data $ xmin < -  data $ xmin + self $ jit 
 if（xmax％in colnames（data））data $ xmax<  -  data $ xmax + self $ jit 
数据
}）
 
 
 
 
 ggplot（datlong，aes（y =估计值，x = Cov，color =物种，组=物种）） + 
 geom_point（position = myjit，size = 1）+ 
 geom_errorbar（aes（ymin = Estimate-SE，ymax =估计+ 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对象 fixJitter 。

以下是情节：

The reproducible data below contains 50 observations for each animal (cat and dog) for each season (Summer and Winter) for two covariates (cov1 and cov2) and their respective error estimates (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

Below I gather the data into long format for ggplot

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

I am trying to plot all points and am using position_jitterdodge to dodge and jitter the points (as suggested in this SO post), but cannot correctly align the error bars with the respective points as shown below. position_dodge correctly aligns points and error bars, but jitter is needed to reduce overlap along the x-axis. Any suggestions would be greatly appreciated.

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"))

解决方案

You can extend the position_dodge to generate a fix jitter for the data:

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"))

Note that you have to create a new object fixJitter for every plot.

Here is the plot:

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