SPATA2: The 'SPATA2' - class

In kueckelj/SPATA2: A Toolbox for Spatial Expression Analysis

The SPATA2 - class

Description

This 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.

Slots

assays

A named list of MolecularAssay objects containing molecular data. Names correspond to slot @modality of the respective molecular modality.

compatibility

A list for compatibility information and data.

data_add

A list for additional data that has not yet a fixed slot in SPATA2 architecture.

dim_red

A list containing dimensionality reduction results.

logfile

A data frame containing logfile data.

meta_obs

A 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_sample

A list providing additional information about the tissue and the tissue donor.

platform

A 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_info

A list containing object information such as default instructions and directories.

sample

A character value. The name of the sample and the SPATA2 object.

spatial

An object of class SpatialData storing coordinates of the observations, images, required transformations for alignment, scale factors, SpatialAnnotation objects, SpatialTrajectory objects, etc.

version

A list specifying versioning details.

kueckelj/SPATA2 documentation built on Feb. 27, 2025, 1:45 p.m.