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# ggalign <a href="https://yunuuuu.github.io/ggalign/"><img src="man/figures/logo.png" align="right" height="139" alt="ggalign website" /></a>
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[![Codecov test
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[![CRAN
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status](https://www.r-pkg.org/badges/version/ggalign)](https://CRAN.R-project.org/package=ggalign)
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[![Project Status: Active - The project has reached a stable, usable
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state and is being actively
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developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
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[![](https://cranlogs.r-pkg.org/badges/ggalign)](https://cran.r-project.org/package=ggalign)
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[![DOI](https://zenodo.org/badge/828195668.svg)](https://doi.org/10.5281/zenodo.14825328)
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The `ggalign` package extends `ggplot2` to simplify the creation of
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complex, multi-plot visualizations. Built on the familiar grammar of
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graphics, it provides intuitive tools to align and organize plots—such
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as heatmaps, dendrograms, or circular layouts—while handling intricate
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relationships in multi-omics data, like genomics or microbiomes. Whether
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you need to stack plots, arrange them around a central figure, or link
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diverse datasets (e.g., genes to pathways), `ggalign` offers flexibility
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and precision with minimal effort.
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## Why use `ggalign`?
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`ggalign` focuses on aligning observations across multiple plots. If
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you’ve ever struggled with aligning plots with self-contained ordering
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(like dendrogram), or applying consistent grouping or ordering across
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multiple plots (e.g., with k-means clustering), `ggalign` is designed to
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make this easier. The package integrates seamlessly with ggplot2,
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providing the flexibility to use its geoms, scales, and other components
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for complex visualizations.
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## Installation
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You can install `ggalign` from `CRAN` using:
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``` r
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install.packages("ggalign")
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```
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Alternatively, install the development version from
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[r-universe](https://yunuuuu.r-universe.dev/ggalign) with:
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``` r
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install.packages("ggalign",
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repos = c("https://yunuuuu.r-universe.dev", "https://cloud.r-project.org")
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)
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```
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or from [GitHub](https://github.com/Yunuuuu/ggalign) with:
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``` r
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# install.packages("remotes")
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remotes::install_github("Yunuuuu/ggalign")
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```
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## Learning ggalign
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1. The complete tutorial is available at:
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<https://yunuuuu.github.io/ggalign-book/>
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2. For the full reference documentation, visit:
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<https://yunuuuu.github.io/ggalign/>
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## Examples
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![](man/figures/overview.png)
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## Compare with other similar tools
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<table class="table"><thead>
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<tr>
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<th colspan="2"></th>
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<th> <code>ggalign</code> </th>
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<th> <code>marsilea</code> </th>
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<th> <code>ComplexHeatmap</code> </th>
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</tr></thead>
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<tbody>
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<tr>
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<td colspan="2"> <strong>Language</strong> </td>
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<td>R</td>
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<td>Python</td>
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<td>R</td>
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</tr>
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<tr>
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<td colspan="2"> <strong>User Interface</strong> </td>
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<td>Declarative</td>
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<td>Declarative</td>
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<td>Functional</td>
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</tr>
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<tr>
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<td colspan="2"> <strong>Plot System</strong> </td>
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<td>ggplot2 (Advanced plot system built on grid system)</td>
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<td>Matplotlib</td>
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<td>grid</td>
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</tr>
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<tr>
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<td colspan="2"> <strong>Focus</strong> </td>
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<td>Composable Visualization</td>
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<td>Composable Visualization</td>
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<td>Heatmap</td>
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</tr>
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<tr>
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<td colspan="2"> <strong>StackLayout</strong> </td>
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<td>✅</td>
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<td>✅</td>
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<td>✅</td>
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</tr>
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<tr>
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<td colspan="2"> <strong>QuadLayout</strong> </td>
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<td>✅</td>
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<td>✅</td>
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<td>Heatmap Only (discrete variables)</td>
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</tr>
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<tr>
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<td colspan="2"> <strong>CircleLayout</strong> </td>
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<td>✅</td>
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<td>❌</td>
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<td>❌</td>
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</tr>
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<tr>
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<td rowspan="4"> <strong>Relationship</strong> </td>
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<td> <strong>One-to-One</strong> </td>
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<td>✅</td>
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<td>✅</td>
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<td>✅</td>
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</tr>
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<tr>
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<td> <strong>One-to-Many</strong>/<strong>Many-to-One</strong> </td>
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<td>✅</td>
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<td>❌</td>
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<td>❌</td>
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</tr>
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<tr>
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<td> <strong>Many-to-Many</strong> </td>
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<td>✅</td>
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<td>❌</td>
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<td>❌</td>
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</tr>
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<tr>
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<td> <strong>Crosswise</strong> </td>
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<td>✅</td>
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<td>❌</td>
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<td>❌</td>
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</tr>
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<tr>
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<td colspan="2"> <strong>Annotate observations</strong> </td>
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<td>✅</td>
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<td>❌</td>
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<td>✅</td>
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</tr>
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<tr>
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<td colspan="2"> <strong>Fully Compatible with ggplot2</strong> </td>
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<td>✅</td>
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<td>❌</td>
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<td>❌</td>
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</tr>
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</tbody></table>
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## Comparison of specifications with other similar tools
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| Specification | `ggalign` | `marsilea` | `ComplexHeatmap` |
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|----------------------------------------------|-------------------------------------------------------|---------------|-------------------------------------------------------|
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| **Reorder observations** | ✅ | ✅ | Heatmap Only |
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| **Group observations into different panels** | ✅ | ✅ | Heatmap Only |
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| **Clustering algorithm** | Kmeans,Hierarchical Clustering and arbitary algorithm | ❌ | Kmeans,Hierarchical Clustering and arbitary algorithm |
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| **Legends Creation** | Automatic | Automatic | Limited automatic, requires manual add |
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| **Legends Position** | Anywhere, can be controlled for a single plot | Anywhere | Four sides, can only be placed on one side at a time |
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| **Dendrogram** | Tree from both `hclust` or `ape` | `hclust` only | `hclust` only |
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| **Tanglegram** | ✅ | ❌ | ❌ |
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| **3D Heatmap** | ✅ | ❌ | ✅ |
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| **Oncoplot** | ✅ | ✅ | ✅ |
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| **UpSet plot** | ✅ | ✅ | ✅ |
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## Altmetric scores
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<script type="text/javascript" src="https://d1bxh8uas1mnw7.cloudfront.net/assets/embed.js"></script>
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<div class="altmetric-embed" data-badge-type="medium-donut"
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data-badge-popover="right" data-altmetric-id="173956809">
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</div>
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## Acknowledgements
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I would like to express my sincere gratitude to the contributors of the
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`ggplot2` project for providing a powerful and flexible framework for
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data visualization in R. Their work laid the foundation for the
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functionality and design of this package. I would also like to thank the
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`patchwork` project, from which the core coding for the plot composer
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was adapted. The `patchwork` library provided a useful mechanism for
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combining and aligning plots, which was modified to suit the needs of
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this package. Without the contributions of these open-source projects,
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this package would not have been possible.
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Additionally, I would like to extend my heartfelt thanks to
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`@teunbrand`, who has fulfilled my numerous feature requests, and
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assisted with the integration of new functions into ggplot2.

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