plotGeneViolin: Plot violin plots for gene expression

In rliger: Linked Inference of Genomic Experimental Relationships

Plot violin plots for gene expression

Description

Generates violin plots of expression of specified gene for each dataset.

Usage

plotGeneViolin(
  object,
  gene,
  methylation.indices = NULL,
  by.dataset = TRUE,
  return.plots = FALSE
)

Arguments

object	liger object.
gene	Gene for which to plot relative expression.
methylation.indices	Indices of datasets in object with methylation data (this data is not magnified and put on log scale).
by.dataset	Plots gene expression for each dataset separately (default TRUE).
return.plots	Return ggplot objects instead of printing directly to console (default FALSE).

Value

List of ggplot plot objects (only if return.plots TRUE, otherwise prints plots to console).

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
ligerex <- optimizeALS(ligerex, k = 5, max.iter = 2)
ligerex <- quantile_norm(ligerex)
ligerex <- louvainCluster(ligerex)
plotGeneViolin(ligerex, "CD74", by.dataset = FALSE)
plotGeneViolin(ligerex, "CD74")

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