README.md

ggalign

This package extends ggplot2 by providing advanced tools for aligning and organizing multiple plots, particularly those that automatically reorder observations, such as dendrogram. It offers fine control over layout adjustment and plot annotations, enabling you to create complex, publication-quality visualizations while still using the familiar grammar of ggplot2.

Why use ggalign?

ggalign focuses on aligning observations across multiple plots. It leverages the "number of observations" in the vctrs package or NROW() function to maintain consistency in plot organization.

If you’ve ever struggled with aligning plots with self-contained ordering (like dendrogram), or applying consistent grouping or ordering across multiple plots (e.g., with k-means clustering), ggalign is designed to make this easier. The package integrates seamlessly with ggplot2, providing the flexibility to use its geoms, scales, and other components for complex visualizations.

Installation

You can install ggalign from CRAN using:

install.packages("ggalign")

Alternatively, install the development version from r-universe with:

install.packages("ggalign",
    repos = c("https://yunuuuu.r-universe.dev", "https://cloud.r-project.org")
)

or from GitHub with:

# install.packages("remotes")
remotes::install_github("Yunuuuu/ggalign")

Learning ggalign

1. The complete tutorial is available at: https://yunuuuu.github.io/ggalign-book/

2. For the full reference documentation, visit: https://yunuuuu.github.io/ggalign/

Compare with other similar tools

	ggalign	ComplexHeatmap	marsilea	ggheatmap	ggtree
Language	R	R	Python	R	R
User Interface	Declarative	Functional	Declarative	Functional	Declarative
Plot System	ggplot2 (Advanced plot system built on grid system)	grid	seaborn	ggplot2	ggplot2 (Advanced plot system built on grid system)
Focus	Composable Visualization	Heatmap	Composable Visualization	Heatmap	tree Data
Heatmap Layout	Yes	Yes	Yes	Yes	No
Marginal Layout	Yes	No	Yes	No	No
Stack Layout	Yes	Yes	Yes	No	No
Circle Layout	Yes	No	No	No	Yes
Cross Layout	Yes	No	No	No	No
Group or Reorder Heatmap	Yes	Yes	Yes	Yes	No
Group or Reorder Stack Only	Yes	No	Yes	No	No
Separate Group into Slices	Yes	Yes	Yes	No	No
Data input	Various, and can be easily extended	fixed	fixed	fixed	Various, and can be easily extended
Visualization Type	Wide variety, provided by ggplot2	Many, but limited	Many, but limited	Limited	Limited Geometric layers support
Legends Creation	Automatic	Limited automatic, requires manual add	Manual	Automatic	Automatic
Legends Position	Anywhere, can be controlled for a single plot	Four sides, can only be placed on one side at a time	?	Four sides, can only be placed on one side at a time	Anywhere
Scientific Color Palettes	Many	Limited	Limited	Many	Many
Tanglegram	Yes	No	Yes	No	No
Dendrogram Position	Anywhere	Heatmap only	Anywhere	Heatmap only	Anywhere
3D Heatmap	Yes	Yes	No	No	No
Oncoplot	Yes	Yes	Yes	No	No
Fully Compatible with ggplot2	Yes	No	No	No	Limited Geometric layers support
Ease of Use	Easy for ggplot2 users	Easy for for grid user	Easy for python user	Easy	Easy for ggplot2 users
Interactive	No	Yes	No	No	No