PlotRelativeExpressionViolin: Generate a violin plot plot using relative expression

In VCCRI/Sierra: PolyA counting and differential transcript usage analysis for scRNA-seq data

Generate a violin plot plot using relative expression

Description

Given two or more peaks to plot, a relative expression score and generate a violin plot according to cell identities

Usage

PlotRelativeExpressionViolin(
  peaks.object,
  peaks.to.plot,
  do.plot = FALSE,
  figure.title = NULL,
  return.plot = TRUE,
  pt.size = 0.5,
  col.set = NULL,
  txt.size = 14,
  add.jitter = TRUE,
  jitter.pt.size = 0.25,
  p.count = 1
)

Arguments

peaks.object	Peak object of either Seurat or SCE class
peaks.to.plot	Set of peaks to plot
do.plot	Whether to plot to output (TRUE by default)
figure.title	Optional figure title
return.plot	Boolean of whether to return plot (default TRUE)
pt.size	size of the points on the t-SNE plot
col.set	default NULL
txt.size	size of text. Default 14
add.jitter	whether to add a geom_jitter to the plot (default: TRUE)
jitter.pt.size	size of point for geom_jitter (default = 0.25)
p.count	Pseudo count

Value

a ggplot2 object

Examples

## Load example data for two peaks from the Cxcl12 gene
extdata_path <- system.file("extdata",package = "Sierra")
load(paste0(extdata_path, "/Cxcl12_example.RData"))
load(paste0(extdata_path, "/TIP_cell_info.RData"))

## Create an SCE object holding the peak data
peaks.sce <- NewPeakSCE(peak.data = peak.counts, 
                        annot.info = peak.annotations, 
                        cell.idents = tip.populations, 
                        tsne.coords = tip.tsne.coordinates,
                        min.cells = 0, min.peaks = 0)
                        
## Plot relative expression of example peaks on t-SNE coordinates
PlotRelativeExpressionViolin(peaks.object = peaks.sce, 
      peaks.to.plot = c("Cxcl12:6:117174603-117175050:1", "Cxcl12:6:117180974-117181367:1"))

VCCRI/Sierra documentation built on July 3, 2023, 6:39 a.m.