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.