setPcaDf: Set dimensional reductions data.frames

In kueckelj/SPATA2: A Toolbox for Spatial Gene 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, of_sample = "", fdb_fn = "stop")

setTsneDf(object, tsne_df, of_sample = "")

setUmapDf(object, umap_df, of_sample = "")

Arguments

object	A valid spata-object.
pca_df, tsne_df, umap_df	The data.frame composed of the variables barcodes, sample and the variables containing the barcode- spot embedding.
of_sample	This argument is currently inactive. It might be reactivated when spata-objects can store more than one sample.

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.

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