setPcaDf: Set dimensional reductions data.frames

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Set dimensional reductions data.frames

Description

Safely adds data.frames containing the barcode-spot embedding of different dimensional reduction techniques. Cell embedding variables must be named as follows:

• pca_df: PC1, PC2, PC3, ...

• tsne_df: tsne1, tsne2, ...

• umap_df: umap1, umap2, ...

Usage

setPcaDf(object, pca_df, fdb_fn = "stop")

setTsneDf(object, tsne_df, ...)

setUmapDf(object, umap_df, ...)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
pca_df, tsne_df, umap_df	The data.frame composed of the variables barcodes, sample and the variables containing the barcode- spot embedding.
...	Used to absorb deprecated arguments or functions.

Details

All set*()-functions offer a save way to set certain slots of your spata-object. They do check the input for validity but effectively overwrite everything that is occupying the slot to be set - use with caution.

Value

A spata object containing the set input.

theMILOlab/SPATA2 documentation built on June 1, 2025, 9:11 p.m.