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https://github.com/corybrunson/ggalluvial
ggplot2 extension for alluvial plots
https://github.com/corybrunson/ggalluvial
alluvial-diagrams alluvial-plots categorical-data-visualization ggplot2 r repeated-measures-data
Last synced: 20 days ago
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ggplot2 extension for alluvial plots
- Host: GitHub
- URL: https://github.com/corybrunson/ggalluvial
- Owner: corybrunson
- License: gpl-3.0
- Created: 2016-05-20T17:34:43.000Z (over 8 years ago)
- Default Branch: main
- Last Pushed: 2023-07-09T19:18:13.000Z (over 1 year ago)
- Last Synced: 2024-05-21T02:53:23.168Z (6 months ago)
- Topics: alluvial-diagrams, alluvial-plots, categorical-data-visualization, ggplot2, r, repeated-measures-data
- Language: R
- Homepage: http://corybrunson.github.io/ggalluvial/
- Size: 120 MB
- Stars: 478
- Watchers: 13
- Forks: 34
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
# ggalluvial
[](https://travis-ci.org/corybrunson/ggalluvial)
[](https://cran.r-project.org/package=ggalluvial)
[](https://cran.r-project.org/package=ggalluvial)
[](https://doi.org/10.5281/zenodo.3836748)
[](https://doi.org/10.21105/joss.02017)
This is a [**ggplot2** extension](https://exts.ggplot2.tidyverse.org/)
for alluvial plots.
## Design
The alluvial plots implemented here can be used to visualize frequency
distributions over time or frequency tables involving several
categorical variables. The design is inspired by the
[**alluvial**](https://github.com/mbojan/alluvial) package, but the
**ggplot2** framework induced several conspicuous differences:
- **alluvial** understands a variety of inputs (vectors, lists, data
frames), whereas **ggalluvial** requires a single data frame;
- **alluvial** uses each variable of these inputs as a dimension of
the data, whereas **ggalluvial** requires the user to specify the
dimensions, either as separate aesthetics or as [key-value
pairs](https://tidyr.tidyverse.org/);
- **alluvial** produces both the *alluvia*, which link cohorts across
multiple dimensions, and (what are here called) the *strata*, which
partition the data along each dimension, in a single function;
whereas **ggalluvial** relies on separate layers (stats and geoms)
to produce strata, alluvia, and alluvial segments called *lodes* and
*flows*.
Additionally, **ggalluvial** arranges these layers vertically without
gaps, so that the secondary plotting axis indicates the cumulative
values of the strata at each dimension.
## Installation
The latest stable release can be installed from CRAN:
``` r
install.packages("ggalluvial")
```
The [`cran` branch](https://github.com/corybrunson/ggalluvial/tree/cran)
will contain the version most recently submitted to
[CRAN](https://cran.r-project.org/package=ggalluvial). It is duplicated
in the `master` branch, from which source the
[website](https://corybrunson.github.io/ggalluvial/) is built.
The development version can be installed from the (default) `main`
branch on GitHub:
``` r
remotes::install_github("corybrunson/ggalluvial@main", build_vignettes = TRUE)
```
Note that, in order to build the vignettes, the imported packages
**alluvial**, **ggfittext**, and **ggrepel** must be installed. To skip
this step, leave `build_vignettes` unspecified or set it to `FALSE`.
The [`optimization`
branch](https://github.com/corybrunson/ggalluvial/tree/optimization)
contains a development version with experimental functions to reduce the
number or area of alluvial overlaps (see issue
[\#6](https://github.com/corybrunson/ggalluvial/issues/6)). Install it
as follows:
``` r
remotes::install_github("corybrunson/ggalluvial", ref = "optimization")
```
Note, however, that this branch has not kept pace with the `main` branch
or with recent upgrades on CRAN.
## Usage
### Example
Here is how to generate an alluvial plot representation of the
multi-dimensional categorical dataset of passengers on the Titanic:
``` r
titanic_wide <- data.frame(Titanic)
head(titanic_wide)
#> Class Sex Age Survived Freq
#> 1 1st Male Child No 0
#> 2 2nd Male Child No 0
#> 3 3rd Male Child No 35
#> 4 Crew Male Child No 0
#> 5 1st Female Child No 0
#> 6 2nd Female Child No 0
ggplot(data = titanic_wide,
aes(axis1 = Class, axis2 = Sex, axis3 = Age,
y = Freq)) +
scale_x_discrete(limits = c("Class", "Sex", "Age"), expand = c(.2, .05)) +
xlab("Demographic") +
geom_alluvium(aes(fill = Survived)) +
geom_stratum() +
geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
theme_minimal() +
ggtitle("passengers on the maiden voyage of the Titanic",
"stratified by demographics and survival")
```
The data is in “wide” format, but **ggalluvial** also recognizes data in
“long” format and can convert between the two:
``` r
titanic_long <- to_lodes_form(data.frame(Titanic),
key = "Demographic",
axes = 1:3)
head(titanic_long)
#> Survived Freq alluvium Demographic stratum
#> 1 No 0 1 Class 1st
#> 2 No 0 2 Class 2nd
#> 3 No 35 3 Class 3rd
#> 4 No 0 4 Class Crew
#> 5 No 0 5 Class 1st
#> 6 No 0 6 Class 2nd
ggplot(data = titanic_long,
aes(x = Demographic, stratum = stratum, alluvium = alluvium,
y = Freq, label = stratum)) +
geom_alluvium(aes(fill = Survived)) +
geom_stratum() + geom_text(stat = "stratum") +
theme_minimal() +
ggtitle("passengers on the maiden voyage of the Titanic",
"stratified by demographics and survival")
```
### Documentation
For detailed discussion of the data formats recognized by **ggalluvial**
and several examples that illustrate its flexibility and limitations,
read the technical vignette:
``` r
vignette(topic = "ggalluvial", package = "ggalluvial")
```
Several additional vignettes offer detailed solutions to specific needs:
- “Labeling small strata” (`"labels"`) for how to elegantly label
strata of a wide range of heights in an alluvial plot;
- “The Order of the Rectangles” (`"order-rectangles"`) for how to
control the positioning of strata and lodes in an alluvial plot; and
- “Tooltips for ggalluvial plots in Shiny apps” (`"shiny"`) for how to
incorporate alluvial plots into interactive apps.
The object documentation includes several more examples. Use `help()` to
call forth more detail on
- any layer (`stat_*` or `geom_*`),
- the conversion functions (`to_*_form`), and
- the data sets installed with the package (`vaccinations` and
`majors`).
### Short form
For some more digestible guidance on using **ggalluvial**, check out
three cheat sheets and demos by students in Joyce Robbins’s [Exploratory
Data Analysis and Visualization Community Contribution
Project](https://jtr13.github.io/cc21fall2/index.html):
- an
[introduction](https://jtr13.github.io/cc21fall2/ggalluvial-cheatsheet.html)
by Meggie Wen (Chapter 33)
- a [cheat
sheet](https://cheatography.com/seleven/cheat-sheets/ggalluvial/) by
Qingyi Zhang (Chapter 14)
- a [blog about how this package implements alluvial
plots](https://medium.com/@arnavsaxena96/all-about-alluvial-diagrams-21da1505520b)
by Arnav Saxena (Chapter 134)
## Acknowledgments
### Resources
Development of this package benefitted from the use of equipment and the
support of colleagues at [UConn Health](https://health.uconn.edu/) and
at [UF Health](https://ufhealth.org/).
### Contribute
Contributions in any form are more than welcome! Pretty much every fix
and feature of this package derives from a problem or question posed by
someone with datasets or design goals i hadn’t anticipated. See the
[CONTRIBUTING](https://github.com/corybrunson/ggalluvial/blob/main/CONTRIBUTING.md)
file for guidance, and please respect the [Code of
Conduct](https://github.com/corybrunson/ggalluvial/blob/main/CODE_OF_CONDUCT.md).
### Cite
If you use **ggalluvial**-generated figures in publication, i’d be
grateful to hear about it! You can also cite the package according to
`citation("ggalluvial")`.