ModuleTopologyHeatmap

Plots a heatmap of the co-expression network topology of a given module.

ModuleTopologyHeatmap(
  seurat_obj,
  mod,
  matrix = "TOM",
  matrix_name = NULL,
  order_by = "kME",
  high_color = NULL,
  low_color = "white",
  raster = TRUE,
  raster_dpi = 200,
  plot_max = "q99",
  plot_min = 0,
  return_genes = FALSE,
  genes_order = NULL,
  TOM_use = NULL,
  wgcna_name = NULL,
  ...
)

Arguments

seurat_obj

A Seurat object

mod

the name of the co-expression module to plot

matrix

specify which matrix to plot, use 'TOM' (topological overlap matrix) or 'Cor' (correlation matrix), or pass a custom square matrix where the rownames and colnames match the genes in this module

matrix_name

name of the matrix plotted that will be used as the label in the plot legend

order_by

order genes in this module by 'kME' (default) or by 'degree' (sum of all connections to this gene in the co-expression network)

high_color

color used for high values in the heatmap, default is the module's unique color

low_color

color used for low values in the heatmap, default is 'white'

raster

logical indicating whether or not to rasterise the plot

raster_dpi

dpi used for a rasterised plot

plot_max

maximum value to plot on the heatmap, can pass a numeric value or a string indicating the quantile ('q99' would be the 99th percentile)

plot_min

minimum value to plot on the heatmap, can pass a numeric value or a string indicating the quantile ('q1' would be the 1st percentile)

return_genes

logical indicating whether or not to return

genes_order

a character vector of genes to plot in this specific order, this option will override the order_by parameter

TOM_use

The name of the hdWGCNA experiment containing the TOM that will be used for plotting

wgcna_name

The name of the hdWGCNA experiment in the seurat_obj@misc slot

Value

ggplot object containing the ModuleTopologyHeatmap

Details

ModuleTopologyHeatmap generates a triangular heatmap plot showing the network "topology" of a specific co-expression module. Each cell in the heatmap represents a gene-gene pair, and the the heatmap is colored by the strength of the connection between these two genes. By default the genes in this heatmap are ordered in both the rows and the columns based on their importance in the module, ranked either by eigengene-based connectivity (kME) or by network degree.