PlotGraphWithModules {MRPC} | R Documentation |
Plot a graph with nodes in modules indicated by colors
Description
Visualization of a graph with nodes in modules inferred from the clustering dendrogram by PlotDendrogram.
Usage
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. |
Value
-
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
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)