ggalluvial
Alluvial Plots in 'ggplot2'
Alluvial plots use x-splines, sometimes augmented with stacked
histograms, to visualize multi-dimensional or repeated-measures data with
categorical or ordinal variables. They can be viewed as simplified and
standardized Sankey diagrams; see Riehmann, Hanfler, and Froehlich (2005)
This is a ggplot2 extension for alluvial diagrams.
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 derived mostly from the alluvial package, but the ggplot2 framework induced several conspicuous differences:
- alluvial understands a variety of inputs (vectors, lists, data frames), while 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;
- 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.
Installation
The latest stable release can be installed from CRAN:
install.packages("ggalluvial")
The cran branch will contain the version most recently submitted to CRAN.
Development versions can be installed from GitHub:
devtools::install_github("corybrunson/ggalluvial", build_vignettes = TRUE)
The optimization branch contains a development version with experimental functions to reduce the number or area of alluvial overlaps (see issue #6). Install it as follows:
devtools::install_github("corybrunson/ggalluvial", ref = "optimization")
Usage
Here is how to generate an alluvial diagram representation of the multi-dimensional categorical dataset of passengers on the Titanic:
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 0ggplot(data = titanic_wide,aes(axis1 = Class, axis2 = Sex, axis3 = Age,y = Freq)) +scale_x_discrete(limits = c("Class", "Sex", "Age"), expand = c(.1, .05)) +xlab("Demographic") +geom_alluvium(aes(fill = Survived)) +geom_stratum() + geom_text(stat = "stratum", label.strata = TRUE) +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:
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 2ndggplot(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")
Resources
For detailed discussion of the data formats recognized by ggalluvial and several examples that illustrate its flexibility and limitations, read the vignette:
vignette(topic = "ggalluvial", package = "ggalluvial")
The documentation contains several examples; use help() to call forth examples of any layer (stat_* or geom_*).
Feedback
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").
Contribute
Issues and pull requests 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.
News
ggalluvial 0.9.1
Suggest sessioninfo for session_info()
Because the only functional (e.g. out README.md) occurrence of devtools is to call session_info() at the ends of the vignettes, this suggestion and usage are switched to sessioninfo.
markdown formatting
Documentation is slightly reformatted due to switching roxygen syntax to markdown.
z-ordering patch
The internal z-ordering function z_order_aes failed to recognize contiguous segments of alluvia, thereby assigning later segments missing values of 'group' and preventing them from being rendered. This has been corrected.
ggalluvial 0.9.0
geom_alluvium() patch
An occurrence of weight in geom_alluvium() was not updated for v0.8.0 and caused geom_alluvium() to throw an error in some cases. This has been corrected.
geom_flow() patch
An earlier solution to the z-ordering problem sufficed for matched layers (*_alluvium() and *_flow()) but failed for the combination of stat_alluvium() with geom_flow(). This is been corrected in the code for GeomFlow$draw_panel(), though a more elegant and general solution is preferred.
Deprecated parameters removed
The deprecated parameters axis_width (all geom layers) and ribbon_bend (geom_alluvium() and geom_flow()) are removed and an explanatory note added to the layers' documentation.
Vignette on labeling small strata
A vignette illustrating two methods for labeling small strata, using other ggplot2 extensions, is included.
self_adjoin() export
The internal function self_adjoin(), invoked by geom_flow(), is revised, exported, documented, and exemplified.
ggalluvial 0.8.0
Stat layer functionality
- The
weightaesthetic for the threestat_*()functions is replaced by theyaesthetic, so thatscale_y_continuous()will correctly transform the vertical scales of the layers. An example is provided in the documentation forstat_alluvium(). Theyaesthetic must be present in order for scales to be correctly transformed. Theweightparameter is still available but deprecated. - For consistency with the switch from
weighttoy, theaggregate.wtsparameter tostat_alluvium()is replaced withaggregate.y;aggregate.wtsis deprecated.
Alluvial data functionality
- Tests for alluvial format are silenced inside the
stat_*()functions.
ggalluvial 0.7.0
Alluvial data functionality
These changes make the functions that test for and convert between alluvial formats behave more like popular functions in the tidyverse. Some of the changes introduce backward incompatibilities, but most result in deprecation warnings.
- The functions
is_alluvial_*()andto_*()are renamed tois_*_form()andto_*_form()for consistency. Their old names are deprecated. is_alluvial()is deprecated and will be removed in a future version.- The parameter
logicalis deprecated. In a future version, the functionsis_*_form()will only return logical values. - The setting
silent = TRUEnow silences all messages. - The functions
is_*_form()now returnFALSEif any weights are negative, with a message to this effect. - These functions now accept unquoted variable names for the
key,value,id,weight, anddiffuseparameters, using up-to-date rlang and tidyselect functionality. - The
axesparameter inis_alluvia_form()andto_lodes_form()now acceptsdplyr::vars()objects, as indplyr::select_at(). Alternatively, variables can be fed to these functions as indplyr::select(), to be collected byrlang::quos(...)and used as axis variables. Ifaxesis notNULL, then such additional arguments are ignored. - The functions
to_*_form()now merge their internal reshapen data frames with the distilled or diffused variables in a consistent order, placing the distilled or diffused variables to the left.
ggalluvial 0.6.0
CRAN checks for v0.5.0
- The package now
Dependson Rv3.3.0(patch number zero) instead ofv3.3.1. I've been unable to install this version locally, so there is a slight chance of incompatibility that i'll be watchful for going forward. - The grid and alluvial packages are now
Suggestsrather thanImports.
Alluvial data functionality
- Source files and documentation for
is_alluvial_*()andto_*()functions are combined; seehelp("alluvial-data"). is_alluvial_alluvianow prints a message rather than a warning when some combinations of strata are not linked by any alluvia.to_lodes()now has adiffuseparameter to join any original variables to the reformatted data by theidvariable (alluvium). This makes it possible to assign original variables to aesthetics after reformatting, as illustrated in a new example.to_alluvia()now has adistillparameter to control the inclusion of any original variables that vary within values ofidinto the reformatted data, based on a distilling function that returns a single value from a vector.to_lodes()now has a logicaldiscernparameter that usesmake.unique()to make stratum values that appear at different axes distinct. Thestat_*()functions can pass the same parameter internally and print a warning if the data is already in lodes form.
Layer internals
GeomFlow$draw_panel()now begins by restricting tocomplete.cases(), corresponding to flows with both starting and terminating axes. (This is not done inStatFlow$compute_panel(), which would have the effect of excluding missing aesthetic values from legends.)GeomAlluvium$setup_data()now throws a warning if some color or differentiation aesthetics vary within alluvia.- A bug in the processing of a custom
lode.orderingargument byStatAlluvium$compute_panel()has been fixed.
ggalluvial 0.5.0
Backward incompatibilities
The ggalluvial() shortcut function, which included a formula interface, deprecated in version 0.4.0, is removed.
earlier versions
I only started maintaining NEWS.md with version 0.5.0.