plot_module: Module plotting function.

In songw01/MEGENA: Multiscale Clustering of Geometrical Network

Module plotting function.

Description

Extract subnetworks for modules and plot.

Usage

plot_module(output.summary, PFN, subset.module = NULL, node.rename=NULL,
col.names=NULL, gene.set = NULL,color.code = "logFC",show.legend = TRUE,
label.hubs.only = TRUE,hubLabel.col = "red",hubLabel.sizeProp = 0.5,show.topn.hubs = 10,
node.sizeProp = 13,label.sizeProp = 13,label.scaleFactor = 10,label.alpha = 0.5,
layout = "kamada.kawai",output.plot = TRUE,out.dir = "modulePlot")

Arguments

output.summary	output from summary function, "MEGENA.ModuleSummary".
PFN	igraph object retaining PFN topology.
subset.module	A character vector for list of module names to plot. Default = NULL plots all modules in output.summary.
node.rename	NULL or a data.frame with the first column being the node ids in the network and the second column being node names for display purpose, eg, this could be used to map ensembl gene ids to gene symbols.
col.names	NULL or a character vector for list of colors to be used for coloring children modules.
gene.set	A list object containing signatures for customized coloring of nodes in resulting network plot.
color.code	A character vector with matched length to "gene.set", to specify colors for each signature.
label.hubs.only	TRUE/FALSE to show labels for significant hub genes only, or all genes. Defauly is TRUE.
hubLabel.col	Label color for hubs. Default is "red"
show.legend	TRUE/FALSE for showing node legend on the bottom of the figure.
hubLabel.sizeProp	A multiplicative factor to adjust hub label sizes with respect to node size values. Default is 0.5
show.topn.hubs	Maximal number of hubs to label on module subnetwork. Default is 10.
node.sizeProp	A multiplicative factor to adjust node sizes with respect to 90th percentile degree node size. Default is 13
label.sizeProp	A multiplicative factor to adjust node label sizes with respect to 90th percentile degree node size. Default is 13
label.scaleFactor	Overall scale factor to control the final size of node labels appearing in figure. Default is 10.
label.alpha	Transparency value ranging from 0 (transparent) to 1 (solid). Default is 0.5.
layout	Network layout algorithm to apply. Options are: "kamada.kawai", "fruchterman.reingold".
output.plot	logical value. output.plot = TRUE generates figure files under folder, "modulePlot".
out.dir	if output.plot = TRUE, then out.dir is created and resulting figures are exported to .png files to the folder.

Details

Subnetwork plot functionality with application of "ggrepel" package for node labeling. The most effective way to control overall node label size is through label.scaleFactor.

Value

A list object holding ggplot objects for plotted modules.

Author(s)

Won-Min Song

Examples

## Not run: 
rm(list = ls())
library(MEGENA)

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)

pnet.obj <- plot_module(output = output.summary,PFN = g,subset.module = "comp1_2",
	layout = "kamada.kawai",label.hubs.only = FALSE,
	gene.set = list("hub.set" = c("CD3E","CD2")),color.code =  c("red"),
	output.plot = FALSE,out.dir = "modulePlot",col.names = c("grey","grey","grey"),
	hubLabel.col = "black",hubLabel.sizeProp = 1,show.topn.hubs = Inf,show.legend = TRUE)
	
pnet.obj

## End(Not run)

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