spatialHeatmap

spatialHeatmap visualizes cell-, tissue- and organ-specific assay data in spatial anatomical images and supports large-scale data mining and co-visualization of bulk and single-cell data.

Key Features:

• Spatial heatmap plot: Colors spatial features (e.g. tissues) annotated in anatomical images according to measured or predicted abundance levels of biomolecules (e.g. mRNAs) using a color key.
• Single-cell co-visualization: Combines spatial heatmaps with embedding plots of high-dimensional data in composite plots to provide spatial context for tissue-level organization of single-cell data.
• Automated biomolecule identification: Identifies biomolecules with spatially selective abundance patterns.
• Clustering: Identifies clusters of biomolecules sharing similar abundance profiles.
• Image compatibility: Works with adequately formatted anatomical images from public collections or custom images.

Scientific Applications:

• Spatial omics visualization: Visualizes spatial assay data from traditional one-at-a-time assays, bulk omics experiments including RNA-seq and proteomics, and single-cell omics experiments in anatomical images.
• Tissue-level organization analysis: Provides spatial context information for gaining insights into tissue-level organization of single-cell data, or vice versa.
• Spatial pattern discovery: Supports automated identification of biomolecules with spatially selective abundance patterns for understanding biological processes in cell, tissue, and organ organizations.

Methodology:

Colors spatial features annotated in images according to biomolecule abundance levels using a color key; combines spatial heatmaps with embedding plots of high-dimensional data for composite visualization.