MEGENA (version 1.3.7)

plot_subgraph: 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".

Value

A list object holding ggplot object and node annotation table.

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.

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]]
# }