plotGenes: Plot expression of multiple genes

In rliger: Linked Inference of Genomic Experimental Relationships

Plot expression of multiple genes

Description

Uses plotGene to plot each gene (and dataset) on a separate page. It is recommended to call this function into a PDF due to the large number of plots produced.

Usage

plotGenes(object, genes, ...)

Arguments

object	liger object. Should call runTSNE before calling.
genes	Vector of gene names.
...	arguments passed from plotGene

Value

If returning single plot, returns ggplot object; if returning multiple plots; returns list of ggplot objects.

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
ligerex <- optimizeALS(ligerex, k = 5, max.iter = 1)
ligerex <- quantile_norm(ligerex)
ligerex <- runTSNE(ligerex)
plotGenes(ligerex, c("CD74", "NKG7"), pt.size = 1)

rliger documentation built on Nov. 9, 2023, 1:07 a.m.