signature_heatmap: Gene signature heatmap

In cellGeometry: Geometric Single Cell Deconvolution

Gene signature heatmap

Description

Produces a heatmap of genes signatures for each cell subclass using ComplexHeatmap.

Usage

signature_heatmap(
  x,
  type = c("subclass", "group", "groupsplit"),
  top = Inf,
  use_filter = NULL,
  arith_mean = FALSE,
  rank = c("max", "angle"),
  scale = c("none", "max", "sphere"),
  col = rev(hcl.colors(10, "Greens3")),
  text = TRUE,
  fontsize = 6.5,
  outlines = FALSE,
  outline_col = "black",
  subset = NULL,
  add_genes = NULL,
  ...
)

Arguments

x	Either a gene signature matrix with genes in rows and cell subclasses in columns, an object of S3 class 'cellMarkers' generated by cellMarkers(), or an object of class 'deconv' generated by deconvolute().
type	Either "subclass" or "group" specifying whether to show the cell subclass or cell group signature from a 'cellMarkers' or 'deconv' object. "groupsplit" shows the distribution of mean gene expression for the group signature across subclasses.
top	Specifies the number of genes per subclass/group to be displayed.
use_filter	Logical whether to show denoised gene signature.
arith_mean	Logical whether to show log2(arithmetic mean), if calculated, instead of usual mean(log2(counts +1)).
rank	Either "max" or "angle" controlling whether genes (rows) are ordered in the heatmap by max expression (the default) or lowest angle (a measure of specificity of the gene as a cell marker).
scale	Character value controlling scaling of genes: "none" for no scaling, "max" to equalise the maximum mean expression between genes, "sphere" to scale genes to the unit hypersphere where cell subclasses or groups are dimensions.
col	Vector of colours passed to ComplexHeatmap::Heatmap().
text	Logical whether to show values of the maximum cell in each row.
fontsize	Numeric value for font size for cell values when text = TRUE.
outlines	Logical whether to outline boxes with maximum values in each row. This supercedes text.
outline_col	Colour for the outline boxes when outlines = TRUE.
subset	Character vector of groups to be subsetted.
add_genes	Character vector of gene names to be added to the heatmap.
...	Optional arguments passed to ComplexHeatmap::Heatmap().

Value

A 'Heatmap' class object.

cellGeometry documentation built on April 20, 2026, 1:06 a.m.