View source: R/PlotGraphWithModules.R
PlotGraphWithModules | R Documentation |
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,...)
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. |
PlotGraphWithModulesObj
: An object of class "graph" of the graph.
Md Bahadur Badsha (mbbadshar@gmail.com)
1. Badsha MB, Martin EA and Fu AQ (2021). MRPC: An R package for inference of causal graphs. Frontiers in Genetics, 10:651812.
PlotDendrogram
## 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)
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