Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

Abstract

Most tools developed to visualize hierarchically clustered heatmaps generate static images. Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations. Clustergrammer can be used to generate shareable interactive visualizations by uploading a data table to a web-site, or by embedding Clustergrammer in Jupyter Notebooks. The Clustergrammer core libraries can also be used as a toolkit by developers to generate visualizations within their own applications. Clustergrammer is demonstrated using gene expression data from the cancer cell line encyclopedia (CCLE), original post-translational modification data collected from lung cancer cells lines by a mass spectrometry approach, and original cytometry by time of flight (CyTOF) single-cell proteomics data from blood. Clustergrammer enables producing interactive web based visualizations for the analysis of diverse biological data.

Mass Spectrometry Imaging: A Review of Emerging Advancements and Future Insights

“…Following m/z mapping to a biological compound, platforms that can handle high-dimensional biology data sets, such as Clustergrammer, a Web-based tool, help to visualize biology changes in heatmap formats that retain the high-dimensionality of the biological data. 148 These pipelines emphasize the importance of special treatment for imaging data compared to LC-MS data.…”

Knowledge-guided analysis of ‘omics’ data using the KnowEnG cloud platform

“…Thus, a joint emphasis on knowledge-guided analysis of rich, spreadsheet-format data sets as well as full-strength online-accessibility and interoperability stands out as a hallmark of the KnowEnG system. Similarly, while tools such as Clustergrammer 55 and shinyheatmap 56 offer convenient means for visualization of spreadsheets, akin to KnowEnG's Spreadsheet Visualizer module, the unique strength of KnowEnG comes from combining the power of interactive visualization with strong analytics. Popular web-based platforms such as cBioPortal 57 , Genomic Data Commons (GDC) 2 and the UCSC Cancer Genome Browser 58 also offer useful online analysis of spreadsheet data, but these are typically intended for data sets stored on those portals.…”

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea‐land transition

“…The Clustergrammer on‐line software (Fernández et al ., ) was used for the functional analysis heatmap construction, by using a correlation type distance and average linkage.…”