The SpatialMap Class

The SpatialMap object is a representation of single-cell spatial expression data in R. Each object might consist of a project or an experiment, or any collection of image acquisition data. SpatialMaps are made up of Region-class objects, which actually contain cell segmentation results, cell coordinates, expression data, and so on. The SpatialMap project thus provides a container or platform with which to manipulate and analyze this data.

Although SpatialMap is being developed specifically to process CODEX data, it is written with compatibility in mind for other related technologies, including Visium (10x Genomics), Slide-seq, or MIBI.

Platform from which to manipulate and analyze spatial biology data

Slots

regions

A list of regions for this project

analyses

A list of analyses for this project

activeRegions

A list of regions which are "active," or included.

activeAnalysis

The analysis that is active. The special designation "regions" means that activeRegions will be analyzed independently. The name of an Analysis or a metadata column can also be used.

projectMetadata

Contains information about each region, including sample IDs, tissue features, or clinical annotations

projectName

A name or ID for the project

projectSummary

A text description of the project, which may be indexed and searched

settings

A list of basic parameters that assist with plotting, etc. SpatialMap