Welcome to Clustergrammer’s Documentation!¶
The Clustergrammer project consists of web-based tools for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps (see Introduction to Clustergrams). Clustergrammer produces highly interactive visualizations that enable intuitive exploration of high-dimensional data and has several optional biology-specific features (e.g. enrichment analysis; see Biology-Specific Features) to facilitate the exploration of gene-level biological data. The project is free, open-source (all code is available on GitHub), and being actively developed at the Human Immune Monitoring Center and the Ma’ayan Lab at the Icahn School of Medicine at Mount Sinai.
Clustergrammer2 is a WebGL (specifically regl) visualization tool that enables researchers to easily visualize and explore large high-dimensional single-cell datasets (e.g. scRNA-seq data) without the need for traditional dimensionality reduction methods (e.g. t-SNE or UMAP). Please see the tutorial video above and Case Studies and Tutorials for more information.
Case Studies and Examples¶
Clustergrammer was developed to visualize high-dimensional biological data (e.g. genome-wide expression data), but it can also generally be applied to any high-dimensional data. Please refer to the Case Studies and Tutorials and links below for more information:
The Clustergrammer-Widget was presented at JupyterCon 2018.
Please contact Nicolas Fernandez (firstname.lastname@example.org) and Avi Ma’ayan (email@example.com) for support, comments, and suggestions. Users can also visit the discussion forum Clustergrammer2-Gitter.
Please consider supporting Clustergrammer by citing our publication:
Fernandez, N. F. et al. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. Sci. Data 4:170151 doi: 10.1038/sdata.2017.151 (2017).
- Getting Started
- Case Studies and Tutorials
- scRNA-seq Gene Expression 2,700 PBMC
- CITE-seq 7,800 PBMC
- Mouse Organogenesis Cell Atlas 2 Million Cells
- CODEX Single Cell Multiplexed Imaging Dashboard
- Cancer Cell Line Encyclopedia Gene Expression Data
- Lung Cancer Post-Translational Modification and Gene Expression Regulation
- Single Cell CyTOF Dataset
- Large Network: Kinase Substrate Similarity Network
- Machine Learning and Miscellaneous Datasets
- Interacting with the Visualization
- Clustergrammer2 Video Tutorial
- Introduction to Clustergrams
- Zooming and Panning
- Mouseover Interactions
- Sidebar Interactions
- Row and Column Reordering
- Interactive Dimensionality Reduction
- Interactive Dendrogram
- Interactive Categories
- Download Icon
- Snapshot Icon
- Opacity Slider
- Row Searching
- Sharing your Interactive Heatmap
- Biology-Specific Interactions
- Biology-Specific Features
- Matrix Formats and Input/Output
- App Integrations