plot_subgraph: subnetwork plotting functionality.

In songw01/MEGENA: Multiscale Clustering of Geometrical Network

subnetwork plotting functionality.

Description

A modification of plot_module() function for more general subnetwork plotting purpose.

Usage

plot_subgraph(module,hub = NULL,PFN,node.default.color = "black",
gene.set = NULL,color.code = "grey",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,layout = "kamada.kawai")

Arguments

module	A character vector containing gene names to be subsetted.
hub	If provided, genes in hub will be highlighted as triangles in resulting figure.
PFN	igraph object retaining PFN topology.
node.default.color	Default node colors for those that do not intersect with signatures in gene.set.
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.
show.legend	TRUE/FALSE for showing node legend on the bottom of the figure.
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"
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.
layout	Network layout algorithm to apply. Options are: "kamada.kawai", "fruchterman.reingold".

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 object and node annotation table.

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_subgraph(module = output.summary$modules[[1]],
hub = c("CD3E","CD2"),PFN = g,node.default.color = "black",
gene.set = NULL,color.code = c("grey"),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,layout = "kamada.kawai")

# the plot	
pnet.obj[[1]]

# the annotation
pnet.obj[[2]]

## End(Not run)

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