signature_heatmap: 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,
  ...
)

Value

A 'Heatmap' class object.

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().