marker_heatmap: Make a heatmap of cell clusters.

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

Make a heatmap of cell clusters.

Description

Make a heatmap of cell clusters.

Usage

marker_heatmap(
  seu,
  markers,
  groups,
  assay = "RNA",
  slot = "data",
  top_n = 5,
  top_n_wt = "fdr",
  title = "Heatmap",
  subtitle = "",
  fill_scale = ggplot2::scale_fill_gradient(low = "white", high = "red"),
  y_text_size = 8,
  angle = 0,
  ...
)

Arguments

seu	A Seurat object.
markers	A dataframe with markers (returned from scran_markers()) or a character vector of gene SYMBOLs.
groups	A character vector: assignment of cells to groups (clusters).
assay, slot, angle, ...	Passed to Seurat::DoHeatmap().
top_n, top_n_wt	Passed to filter_markers(). If top_n is NULL, all markers in markers will be used (SYMBOL column in case markers is a dataframe-like object). If top_n is numeric, markers must be a dataframe-like object.
title	A character scalar: heatmap title.
subtitle	A character scalar: heatmap subtitle.
fill_scale	A Scale object from ggplot2, e.g. ggplot2::scale_fill_gradient(low = "white", high = "red") (default).
y_text_size	A numeric scalar: text size on y-axe of the heatmap.

Value

A named list.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.