plotReducedDim_mod: A wrapper around 'scater::plotReducedDim()'.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

A wrapper around scater::plotReducedDim().

Description

A wrapper around scater::plotReducedDim().

Usage

plotReducedDim_mod(
  sce,
  dimred,
  colour_by = NULL,
  point_size = 1,
  point_alpha = 0.8,
  title = "",
  subtitle = "",
  use_default_ggplot_palette = TRUE,
  colour_gradient = list(low = "lightgrey", high = "blue"),
  legend_title = NULL,
  add_cells_per_cluster = TRUE,
  ...
)

Arguments

sce	A SingleCellExperiment object.
dimred, colour_by, point_size, point_alpha, ...	Passed to scater::plotReducedDim().
title, subtitle, legend_title	A character scalar.
use_default_ggplot_palette	A logical scalar: if TRUE, use the default ggplot2 palette (ggplot2::scale_color_hue()).
colour_gradient	A named list with low and high colors for continuous variables.
add_cells_per_cluster	A logical scalar: if TRUE and colour_by variable is (coercible to) factor, add number of cells per each level to color legend labels.

Value

A ggplot2 object.

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.