SPATA2 - classSPATA2.RdThis S4 class represents a spatial multiomics data object, containing various assays, compatibility information, dimensionality reduction results, histological images, log file data, metadata for observations, additional metadata information, spatial method details, object information, sample identifiers, spatial data, and versioning details.
assaysA named list of MolecularAssay objects containing molecular data. Names
correspond to slot @modality of the respective molecular modality.
compatibilityA list for compatibility information and data.
data_addA list for additional data that has not yet a fixed slot in
SPATA2 architecture.
dim_redA list containing dimensionality reduction results.
logfileA data frame containing logfile data.
meta_obsA data frame containing metadata for the observations. This comprises all variables that are not found in the molecular assays including cluster and grouping variables, summary statistics, etc.
meta_sampleA list providing additional information about the tissue and the tissue donor.
platformA character value. The name of the platform used (e.g. VisiumSmall, VisiumLarge, MERFISH, Xenium).
Should be equal to the name of the SpatialMethod class of slot @method in the SpatialData object.
obj_infoA list containing object information such as default instructions and directories.
sampleA character value. The name of the sample and the SPATA2 object.
spatialAn object of class SpatialData storing coordinates of the observations,
images, required transformations for alignment, scale factors, SpatialAnnotation objects,
SpatialTrajectory objects, etc.
versionA list specifying versioning details.