Academic Journal

Composable Visualization of High-Dimensional Biological Data with ggalign.

Bibliographic Details
Title: Composable Visualization of High-Dimensional Biological Data with ggalign.
Authors: Liu W; Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China.; These authors contributed equally to this work., Ding J; Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China.; These authors contributed equally to this work., Sun Y; Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China., Yan B; Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China., Wang Z; Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China., Wang C; Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China., Shu C; Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China., Zhou JG; Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China., Yu G; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.; These authors jointly supervised this work., Peng Y; Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China.; Department of Urology, Peking University People's hospital, Beijing, China.; These authors jointly supervised this work., Wang S; Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China.; These authors jointly supervised this work.
Source: Current protocols [Curr Protoc] 2026 Sep; Vol. 6 (9), pp. e70453.
Publication Type: Journal Article
Language: English
Journal Info: Publisher: John Wiley & Sons Country of Publication: United States NLM ID: 101773894 Publication Model: Print Cited Medium: Internet ISSN: 2691-1299 (Electronic) Linking ISSN: 26911299 NLM ISO Abbreviation: Curr Protoc Subsets: MEDLINE
Imprint Name(s): Original Publication: Hoboken, NJ : John Wiley & Sons, [2021]-
MeSH Terms: Computational Biology*/methods , Software* , Computer Graphics* , Data Visualization*, Humans ; Multiomics
Abstract: ggalign is an R/CRAN package for creating flexible and composable multi-panel data visualizations. The package extends the ggplot2 grammar of graphics by introducing an integrative framework that supports both data-free and data-aware composition. After five years of continuous development, ggalign has evolved into a comprehensive solution that handles diverse data types and layout structures, including quad, circular, and stack layouts. It was originally designed for general-purpose composable visualization and has been expanded to support multi-omics data integration, extending the application of ggalign to pan-cancer analysis, single-cell transcriptomics, and microbiome studies. This article presents eight basic protocols for constructing complex visualizations using the declarative syntax of ggalign. Basic Protocol 1 describes data-free composition for flexible arrangement of multiple plots; Basic Protocol 2 describes data-aware quad layout for integrating a central plot with surrounding annotations; Basic Protocol 3 describes data-aware circular layout for visualizing ring-structured data; Basic Protocol 4 describes stack layout and nested composition for coordinated display of multi-track graphics; Basic Protocol 5 describes visualization of gene expression matrix heatmaps; Basic Protocol 6 describes visualization of somatic mutation landscapes using ggoncoplot(); Basic Protocol 7 describes circular visualization based on chromosome data, and Basic Protocol 8 describes cross-connection visualization between genes and pathways. The complete package reference is available at https://yunuuuu.github.io/ggalign/, with comprehensive documentation and tutorials at https://yunuuuu.github.io/ggalign-book/, and a gallery of example figures at https://yunuuuu.github.io/ggalign-gallery/. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Data-free composition Basic Protocol 2: Aligning data-aware with quad layouts Basic Protocol 3: Aligning data-aware with circular layouts Basic Protocol 4: Stack layouts and nested composition Basic Protocol 5: Visualizing heatmap of gene expression matrix Basic Protocol 6: Visualizing somatic mutation landscapes using ggoncoplot() Basic Protocol 7: Visualizing circos plots with ggalign Basic Protocol 8: Visualizing observational connections.
(© 2026 Wiley Periodicals LLC.)
References: Dolgalev, I. (2026). msigdbr: MSigDB gene sets for multiple organisms in a tidy data format. R package version 26.1.0.9000, https://igordot.github.io/msigdbr/.
Esteller, M. (2008). Epigenetics in cancer. New England Journal of Medicine, 358, 1148–1159.
Fujita, P. A., Rhead, B., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M. S., Goldman, M., Barber, G. P., Clawson, H., Coelho, A., Diekhans, M., Dreszer, T. R., Giardine, B. M., Harte, R. A., Hillman‐Jackson, J., Hsu, F., Kirkup, V., Kuhn, R. M., Learned, K., … Kent, W. J. (2011). The UCSC Genome Browser database: update 2011. Nucleic Acids Research, 39, D876–D882.
Garnier, S., Ross, N., Rudis, R., Camargo, P. A, Sciaini, M., & Scherer, C. (2024). viridis(Lite)—Colorblind‐Friendly Color Maps for R. https://doi.org/10.5281/zenodo.4679423.
Gu, Z. (2022). Complex heatmap visualization. iMeta, 1, e43.
Gu, Z., Gu, L., Eils, R., Schlesner, M., & Brors, B. (2014). circlize implements and enhances circular visualization with R. Bioinformatics, 30, 2811–2812.
Hoadley, K. A., Yau, C., Hinoue, T., Wolf, D. M., Lazar, A. J., Drill, E., Shen, R., Taylor, A. M., Cherniack, A. D., Thorsson, V., Akbani, R., Bowlby, R., Wong, C. K., Wiznerowicz, M., Sanchez‐Vega, F., Robertson, A. G., Schneider, B. G., Lawrence, M. S., Noushmehr, H., … Laird, P. W. (2018). Cell‐of‐origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer. Cell, 173, 291–304.e6.
Kolde, R. (2025). pheatmap: Pretty heatmaps. R package version 1.0.13, https://CRAN.R‐project.org/package=pheatmap.
Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., & Marra, M. A. (2009). Circos: an information aesthetic for comparative genomics. Genome Research, 19(9), 1639–1645. https://doi.org/10.1101/gr.092759.109.
Laajala, T. D., Sreekanth, V., Soupir, A., Creed, J., Calboli, F. C., Singaravelu, K., Orman, M., Colin‐Leitzinger, C., Gerke, T., Fidley, B. L., Tyekucheva, S., & Costello, J. C. (2023). curatedPCaData: Integration of clinical, genomic, and signature features in a curated and harmonized prostate cancer data resource. bioRxiv: the preprint server for biology, 2023.01.17.524403. https://doi.org/10.1101/2023.01.17.524403.
Mayakonda, A., Lin, D.‐C., Assenov, Y., Plass, C., & Koeffler, H. P. (2018). Maftools: Efficient and comprehensive analysis of somatic variants in cancer. Genome Research, 28, 1747–1756.
Morgan, M., & Shepherd, L. (2026). AnnotationHub: Client to access AnnotationHub resources. R package version 4.3.2, https://bioconductor.org/packages/AnnotationHub.
Neuwirth, E. (2022). RColorBrewer: ColorBrewer Palettes. R package version 1.1‐3, https://CRAN.R‐project.org/package=RColorBrewer.
Pedersen, T. L. (2025). Patchwork: The Composer of Plots. R package version 1.3.2.
Peng, Y., Jiang, S., Song, Y., Luo, P., Li, J., Hu, D., Zhou, J. ‐ G., Yu, G., Xu, T., & Wang, S. (2025). ggalign: Bridging the grammar of graphics and biological multilayered complexity. Advanced Science, 12, e07799.
Ramos, M., Schiffer, L., Re, A., Azhar, R., Basunia, A., Rodriguez Cabrera, C., Chan, T., Chapman, P., Davis, S., Gomez‐Cabrero, D., Culhane, A., Haibe‐Kains, B., Hansen, K., Kodali, H., Louis, M., Mer, A., Reister, M., Morgan, M., Carey, V., & Waldron, L. (2017). Software for the integration of multi‐omics experiments in Bioconductor. Cancer Research, 77(21), e39–42. https://doi.org/10.1158/0008‐5472.CAN‐17‐0344.
Robinson, D., Hayes, A., Couch, S., & Hvitfeldt, E. (2026). broom: Convert statistical objects into tidy tibbles. R package version 1.0.13, https://broom.tidymodels.org/.
Wickham, H. (2010). A layered grammar of graphics. Journal of Computational and Graphical Statistics, 19, 3–28.
Wickham, H. (2011). ggplot2. WIREs Computational Statistics, 3, 180–185.
Wickham, H., François, R., Henry, L., Müller, K., & Vaughan, D. (2026). dplyr: A Grammar of Data Manipulation. R package version 1.2.1.9000, https://github.com/tidyverse/dplyr.
Wickham, H., & Henry, L. (2026). purrr: Functional Programming Tools. R package version 1.2.2, https://purrr.tidyverse.org/.
Xu, S., Wang, Q., Wen, S., Li, J., He, N., Li, M., Hackl, T., Wang, R., Zeng, D., Wang, S., Li, S., Gao, C.‐H., Zhou, L., Tao, S., Xie, Z., Deng, L., & Yu, G. (2025). aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types. The Innovation, 6, 100958.
Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. (2017). ggtree: An r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8, 28–36.
Zheng, Y., Zheng, Z., Rendeiro, A. F., & Cheung, E. (2025). Marsilea: An intuitive generalized paradigm for composable visualizations. Genome Biology, 26, 5.
Grant Information: National Natural Science Foundation of China
Contributed Indexing: Keywords: composable visualization; data visualization; ggalign; grammar of graphics; omics
Entry Date(s): Date Created: 20260921 Date Completed: 20260921 Latest Revision: 20260921
Update Code: 20260921
DOI: 10.1002/cpz1.70453
PMID: 42765627
Database: MEDLINE
FullText Text:
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  Data: Composable Visualization of High-Dimensional Biological Data with ggalign.
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  Data: ggalign is an R/CRAN package for creating flexible and composable multi-panel data visualizations. The package extends the ggplot2 grammar of graphics by introducing an integrative framework that supports both data-free and data-aware composition. After five years of continuous development, ggalign has evolved into a comprehensive solution that handles diverse data types and layout structures, including quad, circular, and stack layouts. It was originally designed for general-purpose composable visualization and has been expanded to support multi-omics data integration, extending the application of ggalign to pan-cancer analysis, single-cell transcriptomics, and microbiome studies. This article presents eight basic protocols for constructing complex visualizations using the declarative syntax of ggalign. Basic Protocol 1 describes data-free composition for flexible arrangement of multiple plots; Basic Protocol 2 describes data-aware quad layout for integrating a central plot with surrounding annotations; Basic Protocol 3 describes data-aware circular layout for visualizing ring-structured data; Basic Protocol 4 describes stack layout and nested composition for coordinated display of multi-track graphics; Basic Protocol 5 describes visualization of gene expression matrix heatmaps; Basic Protocol 6 describes visualization of somatic mutation landscapes using ggoncoplot(); Basic Protocol 7 describes circular visualization based on chromosome data, and Basic Protocol 8 describes cross-connection visualization between genes and pathways. The complete package reference is available at https://yunuuuu.github.io/ggalign/, with comprehensive documentation and tutorials at https://yunuuuu.github.io/ggalign-book/, and a gallery of example figures at https://yunuuuu.github.io/ggalign-gallery/. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Data-free composition Basic Protocol 2: Aligning data-aware with quad layouts Basic Protocol 3: Aligning data-aware with circular layouts Basic Protocol 4: Stack layouts and nested composition Basic Protocol 5: Visualizing heatmap of gene expression matrix Basic Protocol 6: Visualizing somatic mutation landscapes using ggoncoplot() Basic Protocol 7: Visualizing circos plots with ggalign Basic Protocol 8: Visualizing observational connections.<br /> (© 2026 Wiley Periodicals LLC.)
– Name: Ref
  Label: References
  Group: RefInfo
  Data: Dolgalev, I. (2026). msigdbr: MSigDB gene sets for multiple organisms in a tidy data format. R package version 26.1.0.9000, https://igordot.github.io/msigdbr/.<br />Esteller, M. (2008). Epigenetics in cancer. New England Journal of Medicine, 358, 1148–1159.<br />Fujita, P. A., Rhead, B., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M. S., Goldman, M., Barber, G. P., Clawson, H., Coelho, A., Diekhans, M., Dreszer, T. R., Giardine, B. M., Harte, R. A., Hillman‐Jackson, J., Hsu, F., Kirkup, V., Kuhn, R. M., Learned, K., … Kent, W. J. (2011). The UCSC Genome Browser database: update 2011. Nucleic Acids Research, 39, D876–D882.<br />Garnier, S., Ross, N., Rudis, R., Camargo, P. A, Sciaini, M., & Scherer, C. (2024). viridis(Lite)—Colorblind‐Friendly Color Maps for R. https://doi.org/10.5281/zenodo.4679423.<br />Gu, Z. (2022). Complex heatmap visualization. iMeta, 1, e43.<br />Gu, Z., Gu, L., Eils, R., Schlesner, M., & Brors, B. (2014). circlize implements and enhances circular visualization with R. Bioinformatics, 30, 2811–2812.<br />Hoadley, K. A., Yau, C., Hinoue, T., Wolf, D. M., Lazar, A. J., Drill, E., Shen, R., Taylor, A. M., Cherniack, A. D., Thorsson, V., Akbani, R., Bowlby, R., Wong, C. K., Wiznerowicz, M., Sanchez‐Vega, F., Robertson, A. G., Schneider, B. G., Lawrence, M. S., Noushmehr, H., … Laird, P. W. (2018). Cell‐of‐origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer. Cell, 173, 291–304.e6.<br />Kolde, R. (2025). pheatmap: Pretty heatmaps. R package version 1.0.13, https://CRAN.R‐project.org/package=pheatmap.<br />Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., & Marra, M. A. (2009). Circos: an information aesthetic for comparative genomics. Genome Research, 19(9), 1639–1645. https://doi.org/10.1101/gr.092759.109.<br />Laajala, T. D., Sreekanth, V., Soupir, A., Creed, J., Calboli, F. C., Singaravelu, K., Orman, M., Colin‐Leitzinger, C., Gerke, T., Fidley, B. L., Tyekucheva, S., & Costello, J. C. (2023). curatedPCaData: Integration of clinical, genomic, and signature features in a curated and harmonized prostate cancer data resource. bioRxiv: the preprint server for biology, 2023.01.17.524403. https://doi.org/10.1101/2023.01.17.524403.<br />Mayakonda, A., Lin, D.‐C., Assenov, Y., Plass, C., & Koeffler, H. P. (2018). Maftools: Efficient and comprehensive analysis of somatic variants in cancer. Genome Research, 28, 1747–1756.<br />Morgan, M., & Shepherd, L. (2026). AnnotationHub: Client to access AnnotationHub resources. R package version 4.3.2, https://bioconductor.org/packages/AnnotationHub.<br />Neuwirth, E. (2022). RColorBrewer: ColorBrewer Palettes. R package version 1.1‐3, https://CRAN.R‐project.org/package=RColorBrewer.<br />Pedersen, T. L. (2025). Patchwork: The Composer of Plots. R package version 1.3.2.<br />Peng, Y., Jiang, S., Song, Y., Luo, P., Li, J., Hu, D., Zhou, J. ‐ G., Yu, G., Xu, T., & Wang, S. (2025). ggalign: Bridging the grammar of graphics and biological multilayered complexity. Advanced Science, 12, e07799.<br />Ramos, M., Schiffer, L., Re, A., Azhar, R., Basunia, A., Rodriguez Cabrera, C., Chan, T., Chapman, P., Davis, S., Gomez‐Cabrero, D., Culhane, A., Haibe‐Kains, B., Hansen, K., Kodali, H., Louis, M., Mer, A., Reister, M., Morgan, M., Carey, V., & Waldron, L. (2017). Software for the integration of multi‐omics experiments in Bioconductor. Cancer Research, 77(21), e39–42. https://doi.org/10.1158/0008‐5472.CAN‐17‐0344.<br />Robinson, D., Hayes, A., Couch, S., & Hvitfeldt, E. (2026). broom: Convert statistical objects into tidy tibbles. R package version 1.0.13, https://broom.tidymodels.org/.<br />Wickham, H. (2010). A layered grammar of graphics. Journal of Computational and Graphical Statistics, 19, 3–28.<br />Wickham, H. (2011). ggplot2. WIREs Computational Statistics, 3, 180–185.<br />Wickham, H., François, R., Henry, L., Müller, K., & Vaughan, D. (2026). dplyr: A Grammar of Data Manipulation. R package version 1.2.1.9000, https://github.com/tidyverse/dplyr.<br />Wickham, H., & Henry, L. (2026). purrr: Functional Programming Tools. R package version 1.2.2, https://purrr.tidyverse.org/.<br />Xu, S., Wang, Q., Wen, S., Li, J., He, N., Li, M., Hackl, T., Wang, R., Zeng, D., Wang, S., Li, S., Gao, C.‐H., Zhou, L., Tao, S., Xie, Z., Deng, L., & Yu, G. (2025). aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types. The Innovation, 6, 100958.<br />Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. (2017). ggtree: An r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8, 28–36.<br />Zheng, Y., Zheng, Z., Rendeiro, A. F., & Cheung, E. (2025). Marsilea: An intuitive generalized paradigm for composable visualizations. Genome Biology, 26, 5.
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