PlotDendrogram function

Plot a dendrogram and display node groups in colored modules

Generate a dendrogram of nodes with dissimilarity based on topological overlap, and group nodes into modules indicated by colors.

PlotDendrogram(Adj_directed, minModuleSize, groupLabels = " ", 
               dendroLabels = FALSE, hclustHang = 0.03, 
               dendroAddGuide = FALSE, dendroGuideHang = 0.05, 
               dendroMain = "Dendrogram with modules of nodes in colors", ...)

Arguments

• Adj_directed: Adjacency matrix from directed graph
• minModuleSize: Minimum module size.
• groupLabels: Argument for plotDendroAndColors . Labels for the colorings given in colors. The labels will be printed to the left of the color rows in the plot.
• dendroLabels: Argument for plotDendroAndColors . Dendrogram labels.
• hclustHang: Argument hang for plot.hclust . The fraction of the plot height by which labels should hang below the rest of the plot.
• dendroAddGuide: Argument addGuide for plotDendroAndColors . Logical: should vertical "guide lines" be added to the dendrogram plot? The lines make it easier to identify color codes with individual samples.
• dendroGuideHang: Argument guideHang for plotDendroAndColors . The fraction of the dendrogram height to leave between the top end of the guide line and the dendrogram merge height.
• dendroMain: Argument main for plot.hclust . Title of the plot.
• ...: Additional plotting arguments for plotDendroAndColors and plot.hclust .

Returns

A list containing the graph objects as follows:

• PlotDendrogramObj: An object of class "graph" of the estimated graph.
• dynamicColors: A list of colors with corresponding nodes.
• GroupMods: Dynamic tree cut to identify modules whose phenotype profiles are very similar.
• GroupModsColors: A table for number of nodes with corresponding colors.
• Adj_symmetric_matrix: A symmetric matrix from ddjacency matrix of directed 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

MRPC .

Examples

## Not run:

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

# Plot of dendrogram with modules colors of nodes
PlotDendrogramObj <- PlotDendrogram(Adj_directed,
                                    minModuleSize = 5)
## End(Not run)