View source: R/PlotDendrogram.R
PlotDendrogram | R Documentation |
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", ...)
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 |
dendroAddGuide |
Argument |
dendroGuideHang |
Argument |
dendroMain |
Argument |
... |
Additional plotting arguments for plotDendroAndColors and plot.hclust. |
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.
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.
MRPC.
## 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)
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