plotReference: Function to plot reference, colored by cell type

In symphony: Efficient and Precise Single-Cell Reference Atlas Mapping

Function to plot reference, colored by cell type

Description

Function to plot reference, colored by cell type

Usage

plotReference(
  reference,
  as.density = TRUE,
  bins = 10,
  bandwidth = 1.5,
  title = "Reference",
  color.by = "cell_type",
  celltype.colors = NULL,
  show.legend = TRUE,
  show.labels = TRUE,
  show.centroids = FALSE
)

Arguments

reference	Symphony reference object (must have UMAP stored)
as.density	if TRUE, plot as density; if FALSE, plot as individual cells
bins	for density, nbins parameter for stat_density_2d
bandwidth	for density, bandwidth parameter for stat_density_2d
title	Plot title
color.by	metadata column name for phenotype labels
celltype.colors	custom color mapping
show.legend	Show cell type legend
show.labels	Show cell type labels
show.centroids	Plot soft cluster centroid locations

Value

A ggplot object.

symphony documentation built on Nov. 5, 2025, 7:41 p.m.