1 Summary

To plot spatial heatmaps (SHMs), a pair of assay data and anatomical image is required (Zhang et al. 2024). The format of the latter should be annotated Scalable Vector Graphics (aSVG), where spatial features such as cells, tissues, and organs are annotated with unique identifiers. One of the most important features in spatialHeatmap is the support of custom aSVGs, in addition to SVGs from public repositories such as EBI anatomogram. A step-by-step tutorial for creating custom aSVGs is provied here.

2 Funding

This project has been funded by NSF awards: PGRP-1546879, PGRP-1810468, PGRP-1936492.


Zhang, Jianhai, Le Zhang, Brendan Gongol, Jordan Hayes, Alexander T Borowsky, Julia Bailey-Serres, and Thomas Girke. 2024. “SpatialHeatmap: Visualizing Spatial Bulk and Single-Cell Assays in Anatomical Images.” NAR Genomics and Bioinformatics 6 (1): lqae006. https://doi.org/10.1093/nargab/lqae006.