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https://github.com/const-ae/ggsignif
Easily add significance brackets to your ggplots
https://github.com/const-ae/ggsignif
asterisk ggplot-extension ggplot2 rstats significance-stars
Last synced: 5 days ago
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Easily add significance brackets to your ggplots
- Host: GitHub
- URL: https://github.com/const-ae/ggsignif
- Owner: const-ae
- License: gpl-3.0
- Created: 2017-04-03T17:56:42.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2024-08-11T05:11:21.000Z (3 months ago)
- Last Synced: 2024-09-23T00:10:43.436Z (about 2 months ago)
- Topics: asterisk, ggplot-extension, ggplot2, rstats, significance-stars
- Language: R
- Homepage: https://const-ae.github.io/ggsignif/
- Size: 14.5 MB
- Stars: 576
- Watchers: 14
- Forks: 43
- Open Issues: 26
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Citation: CITATION.cff
- Codemeta: codemeta.json
Awesome Lists containing this project
- jimsghstars - const-ae/ggsignif - Easily add significance brackets to your ggplots (R)
README
---
output: github_document
---
# ggsignif: Significance Brackets for 'ggplot2' 
[](https://cran.r-project.org/package=ggsignif)
[](https://github.com/const-ae/ggsignif/actions)
[](https://CRAN.R-project.org/package=ggsignif)
[](https://app.codecov.io/gh/const-ae/ggsignif?branch=main)
[](https://lifecycle.r-lib.org/articles/stages.html)
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
dpi = 300,
out.width = "100%",
fig.path = "man/figures/README-",
message = FALSE,
warning = FALSE
)
```
## Introduction
This package provides an easy way to indicate if two groups are significantly
different. Commonly this is shown by a bar on top connecting the groups of
interest which itself is annotated with the level of significance (NS, \*, \*\*,
\*\*\*). The package provides a single layer (`geom_signif`) that takes the
groups for comparison and the test (t.test, wilcox etc.) and adds the annotation
to the plot.
## Citation
If you wish to cite this package in a publication, you can run the following
command in your R console:
```{r citation}
citation("ggsignif")
```
## Example
You can first install this package from `CRAN`:
```{r eval=FALSE}
install.packages("ggsignif")
```
Or get the latest development version:
```{r eval=FALSE}
install.packages("remotes")
remotes::install_github("const-ae/ggsignif")
```
Plot significance
```{r simpe_comparison}
library(ggplot2)
library(ggsignif)
p1 <- ggplot(mpg, aes(class, hwy)) +
geom_boxplot() +
geom_signif(
comparisons = list(c("compact", "midsize"), c("minivan", "suv")),
map_signif_level = TRUE, textsize = 6
) +
ylim(NA, 48)
p1
```
Control the direction (either `x` or `y`) via `orientation`
```{r orientation_argument}
p2 <- ggplot(
data = mpg,
mapping = aes(
x = hwy,
y = class
)
) +
geom_boxplot(
orientation = "y"
) +
geom_signif(
comparisons = list(
c("compact", "midsize"),
c("minivan", "suv")
),
map_signif_level = TRUE,
textsize = 6,
margin_top = 0.08,
step_increase = 0.05,
tip_length = 0.01,
orientation = "y"
)
p2
```
Compatible with coord_flip
```{r coord_flip}
p1 + coord_flip()
```
Setting the precise location
This is important if you use `position="dodge"`, because in that case I cannot
calculate the correct position of the bars automatically.
```{r dodge_comparison}
# Calculate annotation
anno <- t.test(
iris[iris$Petal.Width > 1 & iris$Species == "versicolor", "Sepal.Width"],
iris[iris$Species == "virginica", "Sepal.Width"]
)$p.value
# Make plot with custom x and y position of the bracket
ggplot(iris, aes(x = Species, y = Sepal.Width, fill = Petal.Width > 1)) +
geom_boxplot(position = "dodge") +
geom_signif(
annotation = formatC(anno, digits = 1),
y_position = 4.05, xmin = 2.2, xmax = 3,
tip_length = c(0.2, 0.04)
)
```
`ggsignif` is compatible with facetting (`facet_wrap` or `facet_grid`). The significance label is calculated for each facet where the axis labels listed in `comparisons` occur. Note that `ggsignif` fails to calculate the significance if the data is grouped globally (e.g., by setting `color`, `fill`, or `group` in `ggplot(aes(...))`). It is fine to group the data per geom (e.g., set the fill within `geom_boxplot(aes(fill = ...)))`.
```{r faceted_simple}
ggplot(diamonds, aes(x = cut, y = carat)) +
geom_boxplot(aes(fill = color)) +
geom_signif(comparisons = list(
c("Fair", "Good"),
c("Very Good", "Ideal")
)) +
facet_wrap(~color) +
ylim(NA, 6.3)
```
## Advanced Example
Sometimes one needs to have a very fine tuned ability to set the location of the
the significance bars in combination with `facet_wrap` or `facet_grid`. In those
cases it you can set the flag `manual=TRUE` and provide the annotations as a
data.frame:
```{r faceted_comparison}
annotation_df <- data.frame(
color = c("E", "H"),
start = c("Good", "Fair"),
end = c("Very Good", "Good"),
y = c(3.6, 4.7),
label = c("Comp. 1", "Comp. 2")
)
annotation_df
ggplot(diamonds, aes(x = cut, y = carat)) +
geom_boxplot() +
geom_signif(
data = annotation_df,
aes(xmin = start, xmax = end, annotations = label, y_position = y),
textsize = 3, vjust = -0.2,
manual = TRUE
) +
facet_wrap(~color) +
ylim(NA, 5.3)
```
You can ignore the warning about the missing aesthetics.
For further details, see:
## Maintenance
This package is provided as is and we currently don't have any plans and the
capacity to add any new features to it. If there is nonetheless a feature which
you would like to see in the package, you are always welcome to submit pull
request, which we will try to address as soon as possible.
## Code of Conduct
Please note that the `ggsignif` project is released with a [Contributor Code of Conduct](https://const-ae.github.io/ggsignif/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.