symphony (version 0.1.2)

plotReference: 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
)

Value

A ggplot object.

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