rliger (version 1.0.1)

plotGenes: 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, ...)

Value

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

Arguments

object

liger object. Should call runTSNE before calling.

genes

Vector of gene names.

...

arguments passed from plotGene

Examples

# \donttest{
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)
# }