loadExampleObject: Load example SPATA2 object

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Load example SPATA2 object

Description

Loads a diet example SPATA2 object.

Usage

loadExampleObject(sample_name, process = FALSE, meta = FALSE, verbose = TRUE)

Arguments

sample_name	Character value. One of c("UKF275T", "UKF313T", "UKF269T", "LMU_MIC").
process	Logical value. If TRUE, the object is processed via: identifyTissueOutline() identifySpatialOutliers() removeSpatialOutliers() normalizeCounts() computeMetaFeatures() using their default setup (in this precise order).
meta	Logical value. If TRUE, adds some meta features like clustering, histological segmentation or copy number variation results to the meta data.frame that has been computed prior to reducing the object to the example version.
verbose	Logical. If TRUE, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Details

The example objects only contain a subsetted count matrix. If you want to work with the complete data sets, use downloadSpataObject().

Value

A reduced diet object of class SPATA2.

Examples

library(SPATA2)

# simply load
object <- loadExampleObject(sample_name = "UKF269T")

# load, process and add some meta data
object_proc <- loadExampleObject(sample_name = "UKF269T", process = TRUE, meta = TRUE)

getMatrixNames(object)
getMatrixNames(object_proc)

plotSurface(object, color_by = "histology") # fails
plotSurface(object_proc, color_by = "histology")

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.