Load example SPATA2 object

Loads a diet example SPATA2 object.

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.)

Value

A reduced diet object of class SPATA2.

Details

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

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")