Plot 2D projection — plotProjection • dreamlet

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
)

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

ggplot2 plot of the projection

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

library(muscat)
library(SingleCellExperiment)

data(example_sce)

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