setDR: Manually set dimension reduction for a channel

In constantAmateur/SoupX: Single Cell mRNA Soup eXterminator

Manually set dimension reduction for a channel

Description

Manually specify the dimension reduction

Usage

setDR(sc, DR, reductName = NULL)

Arguments

sc	A SoupChannel object.
DR	The dimension reduction coordinates (e.g., tSNE). This must be a data.frame, with two columns giving the two dimension reduction coordinates. The data.frame must either have row names matching the row names of sc$metaData, or be ordered in the same order as sc$metaData.
reductName	What to name the reduction (defaults to column names provided).

Value

A modified SoupChannel object for which the dimension reduction has been set.

Examples

sc = load10X(system.file('extdata','toyData',package='SoupX'))
mDat = read.table(system.file('extdata','toyData','metaData.tsv',package='SoupX'),sep='\t')
sc = setDR(sc,mDat[,c('tSNE_1','tSNE_2')])

constantAmateur/SoupX documentation built on Nov. 2, 2022, 10:16 a.m.