ModuleTopologyBarplot: ModuleTopologyBarplot

In smorabit/hdWGCNA: hdWGCNA

ModuleTopologyBarplot

Description

Plots a ranked barplot of genes in a co-expression module by intramodular connectivity

Usage

ModuleTopologyBarplot(
  seurat_obj,
  mod,
  features = "kME",
  plot_color = NULL,
  alpha = TRUE,
  genes_order = NULL,
  return_genes = FALSE,
  wgcna_name = NULL
)

Arguments

seurat_obj	A Seurat object
mod	the name of the co-expression module to plot
features	specify the features to use in the barplot, 'kME' or 'degree' or 'weighted_degree' (degree scaled to 0 or 1)
plot_color	color used for the bar plot, default is the module's unique color
alpha	logical indicating whether or not to add opacity to the barplot based on the strength (kME or degree)
genes_order	a character vector of genes to plot in this specific order, this option will override the order_by parameter
return_genes	logical indicating whether or not to return
wgcna_name	The name of the hdWGCNA experiment in the seurat_obj@misc slot

Details

ModuleTopologyBarplot generates a barplot showing the intramodular connectivity of each gene in a specific co-expression module. Each bar in this plot represents a single gene, and they are ranked based on the strength of their connections within that particular module. A custom gene ordering can be supplied, which is helpful when comparing the module topologies side by side with more than one dataset.

Value

ggplot object containing the ModuleTopologyBarplot

smorabit/hdWGCNA documentation built on July 20, 2024, 8:58 p.m.