英文:
Computed error bars do not plot for factor data in ggplot2 R
问题
I am trying to plot error bars for factor data as shown in this reproducible example here. This example just runs fine. However, I tried the same thing with my original dataset, but error bars refuse to plot. I am a little lost. The following are the relevant pieces of code and as reproducible as possible. Any idea, why I cannot get the error bars to work?
Dataframe df has two columns: yaxis.og and species (4 species) like this:
yaxis.og species<dbl> <fct>1 2.56 A2 3.81 B3 1.48 C4 1.65 D5 -0.177 A.....
I computed a simple linear model and stored the results as such:
summary_df <- summary(mod)$coefficients %>%as_tibble() %>%dplyr::mutate(species = c("A","B","C","D")) %>%dplyr::rename(yaxis = Estimate) %>%mutate(ymin = yaxis - 1.96 * `Std. Error`,ymax = yaxis + 1.96 * `Std. Error`)
When I plot it without error bars, it plots fine:
p <- ggplot(aes(x = species, y = yaxis.og, color = species, group = species), data = df) +geom_jitter(width = 0.1) +geom_point(aes(x = species, y = yaxis), color = 'black', size = 2, data = summary_df)
When I add error bars in, it throws a huge error. The error doesn't make too much sense either because the last layer uses a different dataset, so why would it need yaxis.og?
p + geom_errorbar(aes(x = species, ymin = ymin, ymax = ymax), data = summary_df)
Error in geom_errorbar():
! Problem while computing aesthetics.
ℹ Error occurred in the 3rd layer.
Caused by error in FUN():
! object 'yaxis.og' not found
Backtrace:
- base (local) `
(x) - ggplot2:::print.ggplot(x)
- ggplot2:::ggplot_build.ggplot(x)
- ggplot2:::by_layer(...)
- ggplot2 (local) f(l = layers[[i]], d = data[[i]])
- l$compute_aesthetics(d, plot)
- ggplot2 (local) compute_aesthetics(..., self = self)
- base::lapply(aesthetics, eval_tidy, data = data, env = env)
- rlang (local) FUN(X[[i]], ...)
英文:
I am trying to plot error bars for factor data as shown in this reproducible example here. This example just runs fine. However, I tried the same thing with my original dataset, but errorbars refuse to plot. I am a little lost. The following are the relevant pieces of code and as reproducible as possible. Any idea, why I a cannot get the errorr bars to work?
Dataframe df has two columns: yaxis.og and species (4 species) like this:
yaxis.og species<dbl> <fct>1 2.56 A2 3.81 B3 1.48 C4 1.65 D5 -0.177 A.....
I computed a simple linear model and stored the results as such:
summary_df <- summary(mod)$coefficients %>%as_tibble() %>%dplyr::mutate(species = c("A","B","C","D")) %>%dplyr::rename(yaxis = Estimate) %>%mutate(ymin = yaxis - 1.96 * `Std. Error`,ymax = yaxis + 1.96 * `Std. Error`)yaxis `Std. Error` df `t value` `Pr(>|t|)` species ymin ymax<dbl> <dbl> <dbl> <dbl> <dbl> <chr> <dbl> <dbl>1 0.611 0.145 61.2 4.22 8.21e- 5 A 0.327 0.8952 2.16 0.160 78.0 13.5 3.93e-22 B 1.85 2.473 1.21 0.153 68.7 7.92 2.84e-11 C 0.912 1.514 2.21 0.223 162. 9.89 2.43e-18 D 1.77 2.64
When I plot it without erorrbars, it plots fine:
p <- ggplot(aes(x = species, y = yaxis.og, color = species, group = species), data = df) +geom_jitter(width = 0.1) +geom_point(aes(x = species, y = yaxis), color = 'black', size = 2, data = summary_df)
When I add errorbars in, it throws a huge error. The error doesn't make to much sense either because the last layer uses a different dataset, so why would it need yaxis.og?
p + geom_errorbar(aes(x = species, ymin = ymin, ymax = ymax), data = summary_df)Error in `geom_errorbar()`:! Problem while computing aesthetics.ℹ Error occurred in the 3rd layer.Caused by error in `FUN()`:! object 'yaxis.og' not foundBacktrace:1. base (local) `<fn>`(x)2. ggplot2:::print.ggplot(x)4. ggplot2:::ggplot_build.ggplot(x)5. ggplot2:::by_layer(...)12. ggplot2 (local) f(l = layers[[i]], d = data[[i]])13. l$compute_aesthetics(d, plot)14. ggplot2 (local) compute_aesthetics(..., self = self)15. base::lapply(aesthetics, eval_tidy, data = data, env = env)16. rlang (local) FUN(X[[i]], ...)
答案1
得分: 1
问题在于ggplot()中定义的所有aes都是全局美学，即使没有使用，也会被所有geom图层继承。因此，ggplot2期望每个geom图层使用的数据中应该有一个名为yaxis.og的列，除非你像在geom_point中那样覆盖全局aes。
解决这个问题的一种方法是在geom_errorbar中添加inherit.aes=FALSE，这会阻止继承全局aes，或者通过使用aes(..., y = NULL)来覆盖全局aes。
使用基于iris的一些示例数据：
library(ggplot2)p +geom_errorbar(aes(x = species, ymin = ymin, ymax = ymax, y = NULL),data = summary_df)
p +geom_errorbar(aes(x = species, ymin = ymin, ymax = ymax),data = summary_df, inherit.aes = FALSE)
数据
set.seed(123)df <- data.frame(yaxis.og = c(iris$Sepal.Length, sample(iris$Sepal.Length, 50)),species = rep(c("A", "B", "C", "D"), each = 50))mod <- lm(yaxis.og ~ species - 1, data = df)
英文:
The issue is that all aes defined in ggplot() are global aesthetics and will inherited by all geom layers even if not used. As a result ggplot2 expects a column with name yaxis.og to be present in the data used by each geom layer, except in case you override the global aes as you do e.g. in geom_point.
One option to fix that would be add inherit.aes=FALSE to geom_errorbar which prevents the global aes to be inherited or to override the global aes by using aes(..., y = NULL).
Using some fake example data based on iris:
library(ggplot2)p +geom_errorbar(aes(x = species, ymin = ymin, ymax = ymax, y = NULL),data = summary_df)
<!-- -->
p +geom_errorbar(aes(x = species, ymin = ymin, ymax = ymax),data = summary_df, inherit.aes = FALSE)
<!-- -->
DATA
set.seed(123)df <- data.frame(yaxis.og = c(iris$Sepal.Length, sample(iris$Sepal.Length, 50)),species = rep(c("A", "B", "C", "D"), each = 50))mod <- lm(yaxis.og ~ species - 1, data = df)
通过集体智慧和协作来改善编程学习和解决问题的方式。致力于成为全球开发者共同参与的知识库，让每个人都能够通过互相帮助和分享经验来进步。
评论