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