SpatialFeatureExperiment-class: The SpatialFeatureExperiment class

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

The SpatialFeatureExperiment class

Description

This class inherits from the SpatialExperiment (SPE) class, which in turn inherits from SingleCellExperiment (SCE). SpatialFeatureExperiment stores geometries of spots or cells in sf objects which form columns of a DataFrame which is in turn a column of the int_colData DataFrame of the underlying SCE object, just like reducedDim in SCE. Geometries of the tissue outline, pathologist annotations, and objects (e.g. nuclei segmentation in a Visium dataset) are stored in sf objects in a named list called annotGeometries in int_metadata.

pachterlab/SpatialFeatureExperiment documentation built on March 11, 2024, 11:11 p.m.