get_module_hierarchy_graph: Module Hierarchy Visualization

In songw01/MEGENA: Multiscale Clustering of Geometrical Network

Module Hierarchy Visualization

Description

Utilizes various layout algorithms from ggraph to visualize module hierarchy with desired root.

Usage

  get_module_hierarchy_graph(htbl,max.depth = 5,anchor.mid = NULL,h.scale = NULL,is.circular = TRUE,layout = "dendrogram")

Arguments

htbl	Two column data.frame table capturing module hierarchy. First column is the parent module, and second column is an immediate child module.
max.depth	Maximum number of hierarchy depth to propagate. Default value 5 is often sufficient to capture the entire MEGENA hierarchy.
anchor.mid	Default is NULL. If specified, it is taken as the root module, and its module hierarchy is subsetted.
h.scale	When layout = "dendrogram" is used, it scales the heights of the dendrogram branching points to make the plot less busy.
is.circular	Default is TRUE. If TRUE, circular dendrogram is drawn.
layout	Options are "dendrogram" and "treemap". See ?ggraph for layout option descriptions.
add_names	If TRUE, it adds modules names at respective branching points.

Details

Returns a list containing the results.

Value

A list object with the components:

pobj	ggplot object for the hierarchy graph.
graph.obj	igraph object for the hierarchy graph.
anchor.mid	The root module id.

Author(s)

Won-Min Song

Examples

  ## Not run: 
    rm(list = ls())
    data(Sample_Expression)
    ijw <- calculate.correlation(datExpr[1:100,],doPerm = 2)
    el <- calculate.PFN(ijw[,1:3])
    g <- graph.data.frame(el,directed = FALSE)
    MEGENA.output <- do.MEGENA(g = g,remove.unsig = FALSE,doPar = FALSE,n.perm = 10)
    output.summary <- MEGENA.ModuleSummary(MEGENA.output,
                                           mod.pvalue = 0.05,hub.pvalue = 0.05,
                                           min.size = 10,max.size = 5000,
                                           annot.table = NULL,id.col = NULL,symbol.col = NULL,
                                           output.sig = TRUE)
    tbl = output.summary$module.table
    htbl = tbl[,c("module.parent","module.id")]
    hplot = get_module_hierarchy_graph(htbl,max.depth = 5,anchor.mid = NULL,h.scale = NULL,is.circular = FALSE,layout = "dendrogram",add_names = TRUE)
    print(hplot$pobj)
  
## End(Not run)

songw01/MEGENA documentation built on Jan. 19, 2024, 6:51 p.m.