PlotGraphWithModules function

Plot a graph with nodes in modules indicated by colors

Visualization of a graph with nodes in modules inferred from the clustering dendrogram by PlotDendrogram .

PlotGraphWithModules(Adj_directed, PlotDendrogramObj, 
                     GV, node.size = 8, arrow.size = 5,
                     label.size = 3,alpha = 1,...)

Arguments

• Adj_directed: Adjacency matrix of a graph.
• PlotDendrogramObj: The graphical objects from PlotDendrogram .
• GV: The number of genetic variants (SNPs/indels/CNVs/eQTL) in the input data matrix. For example, if the data has one SNPs/indels/CNV/eQTL in the first column, then GV = 1, if 2 SNPs/indels/CNVs/eQTL in the 1st and 2nd Column, then GV = 2, and so on. If no GV then GV = 0.
• node.size: The size of the nodes in the graph. Defaults to 8.
• arrow.size: The size of the arrows for directed network edges, in points. Defaults to 5.
• label.size: The size of the node labels in points, as a numeric value, a vector of numeric values, or as a vertex attribute containing numeric values. Defaults to 3.
• alpha: The level of transparency of the edges and nodes. Defaults to 1 (no transparency).
• ...: Other arguments passed to ggnet2 .

Returns

• PlotGraphWithModulesObj: An object of class "graph" of the graph.

Author(s)

Md Bahadur Badsha (mbbadshar@gmail.com)

References

1. Badsha MB, Martin EA and Fu AQ (2021). MRPC: An R package for inference of causal graphs. Frontiers in Genetics, 10:651812.

See Also

PlotDendrogram

Examples

## Not run:

# Adjacency matrix from a graph in the example
Adj_directed <- as(data_examples$complex$cont$withGV$graph,
                   "matrix")

# A clustering dendrogram with nodes grouped in colored modules
PlotDendrogramObj <- PlotDendrogram(Adj_directed,
                                    minModuleSize = 5)
                  
# A graph object with nodes in modules
PlotGraphWithModulesObj <- PlotGraphWithModules(Adj_directed,
                                                PlotDendrogramObj,
                                                GV = 14,
                                                node.size = 8,
                                                arrow.size = 5,
                                                label.size = 3,
                                                alpha = 1) 

# Plot the graph with nodes in different colors
plot(PlotGraphWithModulesObj) 
## End(Not run)