embedNewCells: Embed new cells in an existing space

In dibbelab/gficf: Gene Frequency - Inverse Cell Frequency

Embed new cells in an existing space

Description

This function embed new cells in an already existing space. For now it supports only UMAP and t-UMAP. Briefly new cells are first normalized with GF-ICF method but using as ICF weigth estimated on the existing cells and than projected in the existing PCA/LSA space before to be embedded in the already existing UMAP space via umap_transform function.

Usage

embedNewCells(data, x, nt = 2, seed = 18051982, verbose = TRUE, ...)

Arguments

data	list; GFICF object
x	Matrix; UMI counts matrix of cells to embedd.
nt	integer; Number of thread to use (default 2).
seed	integer; Initial seed to use.
verbose	boolean; Icrease verbosity.
...	Additional arguments to pass to Rtsne or umap_transform call.

Value

The updated gficf object.

dibbelab/gficf documentation built on Nov. 2, 2022, 2:28 a.m.