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README.Rmd
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---
output: github_document
params:
book: https://yunuuuu.github.io/ggalign-book/
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
```{r echo=FALSE}
url <- params[["book"]]
```
# ggalign <a href="https://yunuuuu.github.io/ggalign/"><img src="man/figures/logo.png" align="right" height="139" alt="ggalign website" /></a>
<!-- badges: start -->
[](https://github.com/Yunuuuu/ggalign/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/Yunuuuu/ggalign?branch=main)
[](https://CRAN.R-project.org/package=ggalign)
[](https://cran.r-project.org/package=ggalign)
[](https://doi.org/10.5281/zenodo.14825328)
<!-- badges: end -->
The `ggalign` package extends `ggplot2` to simplify the creation of complex,
multi-plot visualizations. Built on the familiar grammar of graphics, it
provides intuitive tools to align and organize plots—such as heatmaps,
dendrograms, or circular layouts—while handling intricate relationships in
multi-omics data, like genomics or microbiomes. Whether you need to stack
plots, arrange them around a central figure, or link diverse datasets (e.g.,
genes to pathways), `ggalign` offers flexibility and precision with minimal
effort.
## Why use `ggalign`?
`ggalign` focuses on aligning observations across multiple plots. 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:
```{r, eval=FALSE}
install.packages("ggalign")
```
Alternatively, install the development version from
[r-universe](https://yunuuuu.r-universe.dev/ggalign) with:
```{r, eval=FALSE}
install.packages("ggalign",
repos = c("https://yunuuuu.r-universe.dev", "https://cloud.r-project.org")
)
```
or from [GitHub](https://github.com/Yunuuuu/ggalign) with:
```{r, eval=FALSE}
# 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/>
## Examples
## Compare with other similar tools
```{=html}
<table class="table"><thead>
<tr>
<th colspan="2"></th>
<th> <code>ggalign</code> </th>
<th> <code>marsilea</code> </th>
<th> <code>ComplexHeatmap</code> </th>
</tr></thead>
<tbody>
<tr>
<td colspan="2"> <strong>Language</strong> </td>
<td>R</td>
<td>Python</td>
<td>R</td>
</tr>
<tr>
<td colspan="2"> <strong>User Interface</strong> </td>
<td>Declarative</td>
<td>Declarative</td>
<td>Functional</td>
</tr>
<tr>
<td colspan="2"> <strong>Plot System</strong> </td>
<td>ggplot2 (Advanced plot system built on grid system)</td>
<td>Matplotlib</td>
<td>grid</td>
</tr>
<tr>
<td colspan="2"> <strong>Focus</strong> </td>
<td>Composable Visualization</td>
<td>Composable Visualization</td>
<td>Heatmap</td>
</tr>
<tr>
<td colspan="2"> <strong>StackLayout</strong> </td>
<td>✅</td>
<td>✅</td>
<td>✅</td>
</tr>
<tr>
<td colspan="2"> <strong>QuadLayout</strong> </td>
<td>✅</td>
<td>✅</td>
<td>Heatmap Only (discrete variables)</td>
</tr>
<tr>
<td colspan="2"> <strong>CircleLayout</strong> </td>
<td>✅</td>
<td>❌</td>
<td>❌</td>
</tr>
<tr>
<td rowspan="4"> <strong>Relationship</strong> </td>
<td> <strong>One-to-One</strong> </td>
<td>✅</td>
<td>✅</td>
<td>✅</td>
</tr>
<tr>
<td> <strong>One-to-Many</strong>/<strong>Many-to-One</strong> </td>
<td>✅</td>
<td>❌</td>
<td>❌</td>
</tr>
<tr>
<td> <strong>Many-to-Many</strong> </td>
<td>✅</td>
<td>❌</td>
<td>❌</td>
</tr>
<tr>
<td> <strong>Crosswise</strong> </td>
<td>✅</td>
<td>❌</td>
<td>❌</td>
</tr>
<tr>
<td colspan="2"> <strong>Annotate observations</strong> </td>
<td>✅</td>
<td>❌</td>
<td>✅</td>
</tr>
<tr>
<td colspan="2"> <strong>Fully Compatible with ggplot2</strong> </td>
<td>✅</td>
<td>❌</td>
<td>❌</td>
</tr>
</tbody></table>
```
## Comparison of specifications with other similar tools
| Specification | `ggalign` | `marsilea` | `ComplexHeatmap` |
| -------------------------------------------- | ----------------------------------------------------- | ------------- | ----------------------------------------------------- |
| **Reorder observations** | ✅ | ✅ | Heatmap Only |
| **Group observations into different panels** | ✅ | ✅ | Heatmap Only |
| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | ❌ | Kmeans,Hierarchical Clustering and arbitary algorithm |
| **Legends Creation** | Automatic | Automatic | Limited automatic, requires manual add |
| **Legends Position** | Anywhere, can be controlled for a single plot | Anywhere | Four sides, can only be placed on one side at a time |
| **Dendrogram** | Tree from both `hclust` or `ape` | `hclust` only | `hclust` only |
| **Tanglegram** | ✅ | ❌ | ❌ |
| **3D Heatmap** | ✅ | ❌ | ✅ |
| **Oncoplot** | ✅ | ✅ | ✅ |
| **UpSet plot** | ✅ | ✅ | ✅ |
## Acknowledgements
I would like to express my sincere gratitude to the contributors of the
`ggplot2` project for providing a powerful and flexible framework for data
visualization in R. Their work laid the foundation for the functionality and
design of this package. I would also like to thank the `patchwork` project, from
which the core coding for the plot composer was adapted. The `patchwork` library
provided a useful mechanism for combining and aligning plots, which was modified
to suit the needs of this package. Without the contributions of these
open-source projects, this package would not have been possible.
Additionally, I would like to extend my heartfelt thanks to `@teunbrand`, who
has fulfilled my numerous feature requests, and assisted with the integration of
new functions into ggplot2.