1 Installation

This package can be installed from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))

2 Class structure

2.1 Introduction

SpatialFeatureExperiment (SFE) is a new S4 class built on top of SpatialExperiment (SPE). SpatialFeatureExperiment incorporates geometries and geometry operations with the sf package. Examples of supported geometries are Visium spots represented with polygons corresponding to their size, cell or nuclei segmentation polygons, tissue boundary polygons, pathologist annotation of histological regions, and transcript spots of genes. Using sf, SpatialFeatureExperiment leverages the GEOS C++ libraries underlying sf for geometry operations, including algorithms for for determining whether geometries intersect, finding intersection geometries, buffering geometries with margins, etc. A schematic of the SFE object is shown below: