3 Bioconductor data classes
3.1 Overview
Bioconductor provides several data classes for storing and manipulating spatial transcriptomics datasets. By relying on these standardized data structures, we can build analysis workflows that can easily connect methods and packages developed by different research groups.
Below, we describe the Bioconductor data classes used in this book.
3.2 SpatialExperiment class
The SpatialExperiment class (Righelli et al. 2022) is the core data class that we use in this book. This class allows us to store datasets at the spot or cell level, i.e. data from sequencing-based platforms (e.g. 10x Genomics Visium) at the spot level, or data from molecule-based platforms that has been aggregated to the cell level.
SpatialExperiment builds on the SingleCellExperiment class (Amezquita et al. 2020) for single-cell RNA sequencing data, with additional customizations to store spatial information, such as spatial coordinates and image files.
A summary of the SpatialExperiment
object structure is shown in the following schematic. Briefly, a SpatialExperiment
object consists of (i) assays
containing expression counts, (ii) rowData
containing information on features, i.e. genes, (iii) colData
containing information on spots or cells, including nonspatial and spatial metadata, (iv) spatialCoords
containing spatial coordinates, and (v) imgData
containing image data. For spot-based data (e.g. 10x Genomics Visium), a single assay
named counts
is used.
For more details, see the SpatialExperiment
package Bioconductor vignette or the paper describing the class (Righelli et al. 2022).
3.3 Molecule-based data
Molecule-based spatial transcriptomics datasets contain additional information, including the spatial coordinates of individual mRNA molecules and segmentation boundaries for cells or nuclei.
The following Bioconductor classes provide additional functionality to store and manipulate this information.
These classes extend SpatialExperiment
and are compatible with SpatialExperiment
for analyses at the aggregated cell level.
3.3.1 MoleculeExperiment
MoleculeExperiment
is available as a Bioconductor package and described by the authors in their paper (Peters Couto et al. 2023).
3.3.2 SpatialFeatureExperiment
SpatialFeatureExperiment
is available as a Bioconductor package and described by the authors in their paper (Moses et al. 2023).