{funkyheatmap} allows generating heatmap-like visualisations for data frames. Funky heatmaps can be fine-tuned by providing annotations of the columns and rows, which allows assigning multiple palettes or geometries or grouping rows and columns together in categories.

Implementations

• JavaScript (incomplete): Repo, npm
• Python: Repo, PyPI, Docs
• R: Repo, CRAN, Docs

Gallery

These are works with funkyheatmap (-inspired) visualisations. Add your work to the list by creating a PR!

Wouter Saelens, Robrecht Cannoodt, Helena Todorov, and Yvan Saeys. 2019. “A Comparison of Single-Cell Trajectory Inference Methods.” Nature Biotechnology. doi: 10.1038/s41587-019-0071-9.

Luecken, Malte D., M. Büttner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, et al. 2021. “Benchmarking Atlas-Level Data Integration in Single-Cell Genomics.” Nature Methods. doi: 10.1038/s41592-021-01336-8.

Mereu, Elisabetta, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J. McCarthy, Adrián Álvarez-Varela, Eduard Batlle, et al. 2020. “Benchmarking Single-Cell RNA-Sequencing Protocols for Cell Atlas Projects.” Nature Biotechnology. doi: 10.1038/s41587-020-0469-4.

Pratapa, Aditya, Amogh P. Jalihal, Jeffrey N. Law, Aditya Bharadwaj, and T. M. Murali. 2019. “Benchmarking Algorithms for Gene Regulatory Network Inference from Single-Cell Transcriptomic Data.” bioRxiv. doi: 10.1101/642926.

Yan, Lulu, and Xiaoqiang Sun. 2022. “Benchmarking and Integration of Methods for Deconvoluting Spatial Transcriptomic Data.” Bioinformatics. doi: 10.1093/bioinformatics/btac805.

Sang-aram, Chananchida, Robin Browaeys, Ruth Seurinck, and Yvan Saeys. 2023. “Spotless: A Reproducible Pipeline for Benchmarking Cell Type Deconvolution in Spatial Transcriptomics,” eLife. doi: 10.7554/eLife.88431.3.