PlotRelativeExpressionUMAP: Generate a t-SNE plot using relative expression

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

Generate a t-SNE plot using relative expression

Description

Given two or more peaks to plot, calculate a relative expression score and plot on UMAP coordinates

Usage

PlotRelativeExpressionUMAP(
  peaks.object,
  peaks.to.plot,
  do.plot = FALSE,
  figure.title = NULL,
  return.plot = TRUE,
  pt.size = 0.5,
  txt.size = 14,
  legend.position = "right",
  use.facet = TRUE,
  p.count = 1
)

Arguments

peaks.object	Seurat object
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. Default 0.5
txt.size	size of text. Default 14
legend.position	position of the legend (right, left, bottom or top)
use.facet	Whether to plot peaks using ggplot facets. If set to FALSE will use cowplot to plot each peak
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
## Note, for this example we are recycling t-SNE coordinates to demonstrate running of the function
peaks.sce <- NewPeakSCE(peak.data = peak.counts, 
                        annot.info = peak.annotations, 
                        cell.idents = tip.populations, 
                        umap.coords = tip.tsne.coordinates,
                        min.cells = 0, min.peaks = 0)
                        
## Plot relative expression of example peaks on t-SNE coordinates
PlotRelativeExpressionUMAP(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.