setDefaultTrajectory: Obtain dimensional reduction data

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Obtain dimensional reduction data

Description

Sets and extracts the default trajectory id. Useful to save typing in functions that require a trajectory name as input.

Usage

getDefaultTrajectory(object, ...)

getDefaultTrajectoryId(object, ...)

setDefaultTrajectory(object, id, verbose = NULL)

setDefaultTrajectoryId(object, id, verbose = NULL)

Arguments

object	A valid spata-object.
id	Character value.
n_pcs	Numeric value. Denotes the number of principal components to be included.

Value

A data.frame that contains the unique identifiers (keys): barcodes, sample and:.

• getPcaDf(): PC1, PC2, PC3, ...PCn

• getTsneDf(): tsne1, tsne2

• getUmapDf(): umap1, umap2

setDefaultTrajectory(): Updated spata object. getDefaultTrajectory(): Character value. Id of the default trajectory.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.