添加第二个geom_points后，重新排序不起作用

Question

我的数据如下：

> head(GEE)

  trait   beta   se       p   analysis signif
1 trait1  0.078 0.01 9.0e-13  group1   1
2 trait2  0.076 0.01 1.7e-11  group1   1
3 trait3  0.063 0.01 1.8e-08  group1   1
4 trait4  0.013 0.01 .06      group1   0
5 trait5  0.018 0.01 .54      group1   0
6 trait6 -0.014 0.01 .64      group1   0

我试图用gglot2绘制一个点和错误条的图，这些点和错误条是在第二列名为beta的列上排序的。下面的代码运行得很好：

ggplot(GEE, aes(y=beta, x=reorder(trait, beta), group=analysis)) + 
  geom_point(aes(color=analysis)) +
  geom_errorbar(aes(ymin=beta-2*se, ymax=beta+2*se,color=analysis), width=.2,
                position=position_dodge(.9)) +
  theme_light() +
  coord_flip() 

但是，我想为重要点添加星号，为此我有一段额外的代码，它成功地将星号添加到重要点：

geom_point(data = GEE[GEE$signif == 1, ],
           color="red",
           shape = "*", 
           size=12, 
           show.legend = F) +

当将它添加到上面的绘图命令中时，完整的命令如下所示：

ggplot(GEE, aes(y=beta, x=reorder(trait, beta), group=analysis)) + 
  geom_point(data = GEE[GEE$signif == 1, ],
             color="red",
             shape = "*", 
             size=12, 
             show.legend = F) +
  geom_point(aes(color=analysis)) +
  geom_errorbar(aes(ymin=beta-2*se, ymax=beta+2*se,color=analysis), width=.2,
                position=position_dodge(.9)) +
  theme_light() +
  coord_flip() 

然而，添加星号后的代码的问题是，它以某种方式取消了我用“x=reorder(特质，beta)”指定的重新排序。现在的秩序完全不同了。为什么？：“

UPDATE：@Lamia在评论中指出，这个问题不能用本文中提供的数据重新产生。本文中的数据只显示来自同一组的顶部行(group1，参见列"analysis")，但在我的完整数据集中有三个组。ggplot2命令用不同的颜色绘制这三个不同的组。只有当我在完整的数据集中阅读所有三个组时，我才能重现这个问题，所以看起来这可能与这个问题有关。

UPDATE 2：正如@Lamia所建议的(对不起，首先应该这么做)，我在下面添加了数据，这些数据再现了问题：

trait,beta,se,p,analysis,signif
trait1,0.078,0.01,9.00E-13,group1,1
trait2,0.076,0.01,1.70E-11,group1,1
trait3,-0.032,0.01,0.004,group1,0
trait4,0.026,0.01,0.024,group1,0
trait5,0.023,0.01,0.037,group1,0
trait1,0.042,0.01,4.50E-04,group2,1
trait2,0.04,0.01,0.002,group2,1
trait3,0.03,0.01,0.025,group2,0
trait4,0.025,0.01,0.078,group2,0
trait5,0.015,0.01,0.294,group2,0
trait1,0.02,0.01,0.078,group3,0
trait2,0.03,0.01,0.078,group3,0
trait3,0.043,0.01,1.90E-04,group3,0
trait4,0.043,0.01,2.40E-04,group3,1
trait5,0.029,0.01,0.013,group3,0

Answer 1

几点建议供考虑..。

ggplot(). 1:在将数据帧输入到之前，先对其进行争论因为属性是一个分类变量，所以可以显式地将其级别指定为一个因素。

library(dplyr)

g2 <- GEE %>%
  mutate(trait = factor(trait, levels = trait[order(beta[analysis == "group1"])]))

> levels(g2$trait)
[1] "trait3" "trait5" "trait4" "trait2" "trait1"

根据第一组的β值，我们可以直观地验证性状的顺序是3-5-4-2-1：

ggplot(GEE, aes(x = beta, y = analysis, label = trait)) + geom_label()

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2:在可能的情况下，只对ggplot()使用一个数据源，这可以确保所有美观的映射链接都是一致的，而且维护起来也更简单。

ggplot(g2, aes(y = beta, x = trait, group = analysis, color = analysis,
               ymin = beta - 2*se, ymax = beta + 2*se)) + 
  geom_point(aes(alpha = signif),   # hide non-significant points while using the same dataset
             color = "red") +       # override 'color = analysis' in ggplot()
  geom_point() +
  geom_errorbar() +
  scale_alpha_identity()

3:对所有相关的geoms重用相同的position_dodge()。再次说明，如果您希望下次更改道奇宽度，则维护起来更简单。

pd <- position_dodge(0.9)

ggplot(g2, aes(y = beta, x = trait, group = analysis, color = analysis,
               ymin = beta - 2*se, ymax = beta + 2*se)) + 
  geom_point(aes(alpha = signif), 
             color = "red", shape = "*", size = 12, show.legend = F,
             position = pd) +
  geom_point(position = pd) +
  geom_errorbar(width=.2, position = pd) +
  scale_alpha_identity() +
  theme_light() +
  coord_flip() 

结果(性状按3-5-4-2-1排序，自下而上)：

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数据：

GEE <- read.csv(
  text = 
"trait,beta,se,p,analysis,signif
trait1,0.078,0.01,9.00E-13,group1,1
trait2,0.076,0.01,1.70E-11,group1,1
trait3,-0.032,0.01,0.004,group1,0
trait4,0.026,0.01,0.024,group1,0
trait5,0.023,0.01,0.037,group1,0
trait1,0.042,0.01,4.50E-04,group2,1
trait2,0.04,0.01,0.002,group2,1
trait3,0.03,0.01,0.025,group2,0
trait4,0.025,0.01,0.078,group2,0
trait5,0.015,0.01,0.294,group2,0
trait1,0.02,0.01,0.078,group3,0
trait2,0.03,0.01,0.078,group3,0
trait3,0.043,0.01,1.90E-04,group3,0
trait4,0.043,0.01,2.40E-04,group3,1
trait5,0.029,0.01,0.013,group3,0")

> levels(GEE$trait) # default order is 1-2-3-4-5
[1] "trait1" "trait2" "trait3" "trait4" "trait5"

Answer 2

试试这个：

library(tidyverse)

GEE <- tribble(
  ~trait, ~beta, ~se, ~p, ~analysis, ~signif,
  "trait1", 0.078, 0.01, 9.0e-13, "group1", 1,
  "trait2", 0.076, 0.01, 1.7e-11, "group1", 1,
  "trait3", 0.063, 0.01, 1.8e-08, "group1", 1,
  "trait4", 0.013, 0.01, .06, "group1", 0,
  "trait5", 0.018, 0.01, .54, "group1", 0,
  "trait6", -0.014, 0.01, .64, "group1", 0
  )

GEE %>% 
  ggplot(aes(y = beta, x = reorder(trait, beta)), group = analysis) +
  geom_point(aes(color = analysis)) +
  geom_errorbar(aes(ymin = beta - 2 * se,
                    ymax = beta + 2 * se,
                    color = analysis,
                    width = 0.2),
                position = position_dodge(0.9)) +
  geom_point(data = GEE[GEE$signif == 1, ],
             color="red",
             shape = "*", 
             size=12, 
             show.legend = F) +
  theme_light() +
  coord_flip()

它改变了这个情节：

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让它看起来像这样：

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这就是你要找的吗？