plot_module_hierarchy: Plot module hierarchy

In MEGENA: Multiscale Clustering of Geometrical Network

Description

visualized module hierarchical structure.

Usage

plot_module_hierarchy(module.table,plot.coord = NULL,
edge.color = "grey",node.color = "black",node.label.color = "black",
label.scaleFactor = 0.5,node.scaleFactor = 0.2,arrow.size = 0.015,
data.col = NULL,low.color = "blue",mid.color = "white",
high.color = "red",mid.value = 0.05)

Arguments

module.table	output from MEGENA.ModuleSummary. Specifically $module.table component of the output.
plot.coord	Two column coordinate matrix. rownames must be labelled according to module.table$id.
edge.color	Edge color to be shown.
node.color	If data.col = NULL, node.color is used to color nodes in figure.
node.label.color	Node label color.
label.scaleFactor	scale number to adjust node label sizes.
node.scaleFactor	scale number to adjust node sizes.
arrow.size	scale number to arrow size.
data.col	A character to specify data vector to color nodes in module.table.
low.color	If data.col != NULL, color to be used in lower value spectrum.
mid.color	If data.col != NULL, color to be used in middle value spectrum.
high.color	If data.col != NULL, color to be used in high value spectrum.
mid.value	If data.col != NULL, value to define middle value spectrum.

Details

Module hierarchy plotting functionality using ggplot2.

Value

A list containing output$hierarchy.obj = ggplot2 object, output$node.data = node attributes, output$edge.data = edge attributes.

Author(s)

Won-Min Song

Examples

## Not run: 
	rm(list = ls())
	data(Sample_Expression)
	ijw <- calculate.correlation(datExpr,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)

	module.table = output.summary$module.table
	colnames(module.table)[1] <- "id"
	output.obj <- plot_module_hierarchy(module.table = module.table,
	label.scaleFactor = 0.15,arrow.size = 0.005,node.label.color = "blue")

	print(output.obj[[1]])

## End(Not run)

MEGENA documentation built on May 1, 2019, 8:07 p.m.