plotProjection: Plot 2D projection

In GabrielHoffman/dreamlet: Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Plot 2D projection

Description

Plot 2D projection (i.e. UMAP, tSNE) for millions of cells efficiently

Usage

plotProjection(
  sce,
  type,
  annotation,
  pointsize = 0,
  pixels = c(512, 512),
  legend.position = "none",
  text = TRUE,
  order
)

Arguments

sce	SingleCellExperiment
type	field in reducedDims(sce) to plot
annotation	column in colData(sce) to annotate each cell
pointsize	Radius of rasterized point. Use 0 for single pixels(fastest).
pixels	Vector with X and Y resolution of the raster, default c(512,512)
legend.position	legend.position: the position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector)
text	show annotation as text. Default TRUE
order	specify order of levels for annotation

Details

Uses scattermore::geom_scattermore() to plot millions of points efficiently

Value

ggplot2 plot of the projection

Examples

library(muscat)
library(SingleCellExperiment)

data(example_sce)

plotProjection(example_sce, "TSNE", "cluster_id", 1)

GabrielHoffman/dreamlet documentation built on May 20, 2024, 2:05 p.m.