{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T16:01:24Z","timestamp":1790438484548,"version":"4.1.0"},"reference-count":24,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":20,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2026,9]]},"abstract":"Abstract<\/jats:title>\n \n ggalign is an R\/CRAN package for creating flexible and composable multi\u2010panel data visualizations. The package extends the ggplot2 grammar of graphics by introducing an integrative framework that supports both data\u2010free and data\u2010aware 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\u2010purpose composable visualization and has been expanded to support multi\u2010omics data integration, extending the application of ggalign to pan\u2010cancer analysis, single\u2010cell 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\u2010free composition for flexible arrangement of multiple plots; Basic Protocol 2 describes data\u2010aware quad layout for integrating a central plot with surrounding annotations; Basic Protocol 3 describes data\u2010aware circular layout for visualizing ring\u2010structured data; Basic Protocol 4 describes stack layout and nested composition for coordinated display of multi\u2010track 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\u2010connection visualization between genes and pathways. The complete package reference is available at\n https:\/\/yunuuuu.github.io\/ggalign\/<\/jats:ext-link>\n , with comprehensive documentation and tutorials at\n https:\/\/yunuuuu.github.io\/ggalign\u2010book\/<\/jats:ext-link>\n , and a gallery of example figures at\n https:\/\/yunuuuu.github.io\/ggalign\u2010gallery\/<\/jats:ext-link>\n . \u00a9 2026 Wiley Periodicals LLC.\n <\/jats:p>\n \n Basic Protocol 1<\/jats:bold>\n : Data\u2010free composition\n <\/jats:p>\n \n Basic Protocol 2<\/jats:bold>\n : Aligning data\u2010aware with quad layouts\n <\/jats:p>\n \n Basic Protocol 3<\/jats:bold>\n : Aligning data\u2010aware with circular layouts\n <\/jats:p>\n \n Basic Protocol 4<\/jats:bold>\n : Stack layouts and nested composition\n <\/jats:p>\n \n Basic Protocol 5<\/jats:bold>\n : Visualizing heatmap of gene expression matrix\n <\/jats:p>\n \n Basic Protocol 6<\/jats:bold>\n : Visualizing somatic mutation landscapes using ggoncoplot()\n <\/jats:p>\n \n Basic Protocol 7<\/jats:bold>\n : Visualizing circos plots with ggalign\n <\/jats:p>\n \n Basic Protocol 8<\/jats:bold>\n : Visualizing observational connections\n <\/jats:p>","DOI":"10.1002\/cpz1.70453","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T12:05:50Z","timestamp":1789992350000},"source":"Crossref","is-referenced-by-count":0,"title":["Composable Visualization of High\u2010Dimensional Biological Data with ggalign"],"prefix":"10.1002","volume":"6","author":[{"given":"Wanyi","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences Central South University Changsha China"},{"name":"These authors contributed equally to this work"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences Central South University Changsha China"},{"name":"These authors contributed equally to this work"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujun","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences Central South University Changsha China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences Central South University Changsha China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhangyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences Central South University Changsha China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyang","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences Central South University Changsha China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenyang","family":"Shu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences Central South University Changsha China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian\u2010Guo","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Oncology The Second Affiliated Hospital of Zunyi Medical University Zunyi China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangchuang","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences Southern Medical University Guangzhou China"},{"name":"These authors jointly supervised this work"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Peng","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences Central South University Changsha China"},{"name":"Department of Urology Peking University People's hospital Beijing China"},{"name":"These authors jointly supervised this work"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shixiang","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences Central South University Changsha China"},{"name":"These authors jointly supervised this work"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"e_1_2_12_2_1","unstructured":"Dolgalev I.(2026).msigdbr: MSigDB gene sets for multiple organisms in a tidy data format. 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