PlotRelativeExpressionBox: Generate a box plot plot using relative expression

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

Generate a box plot plot using relative expression

Description

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

Usage

PlotRelativeExpressionBox(
  peaks.object,
  peaks.to.plot,
  do.plot = FALSE,
  figure.title = NULL,
  return.plot = TRUE,
  pt.size = 0.5,
  col.set = NULL,
  txt.size = 14,
  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 (default True) identifying if plot should be returned.
pt.size	Size of the points on the t-SNE plot (default 0.5)
col.set	col set (default NULL)
txt.size	sie of text (default 14)
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
PlotRelativeExpressionBox(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.