MEGENA (version 1.3.7)

plot_module_hierarchy: Plot module hierarchy

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.

Value

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

Details

Module hierarchy plotting functionality using ggplot2.

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]])
# }