compareWordNet: compareWordNet

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

compareWordNet

Description

Compare multiple networks based on words

Usage

compareWordNet(
  listOfNets,
  titles = NULL,
  layout = "nicely",
  hull = FALSE,
  size = "freq",
  conc = 1,
  tag = FALSE,
  tagLevel = 1,
  edgeLink = TRUE,
  freqMean = FALSE,
  scaleRange = c(5, 10),
  ovlThresh = 0,
  returnNet = FALSE,
  colPal = "Pastel1",
  colorText = FALSE,
  community = FALSE,
  returnClass = TRUE
)

Arguments

listOfNets	list consisting results of wc* functions (plotType="network")
titles	title to be shown on plot
layout	layout
hull	show category by hull
size	node size, freq, overlap or numeric number
conc	concavity parameter
tag	show tag on plot
tagLevel	words that tagged in this many networks will be included
edgeLink	whether to use link or diagonal
freqMean	how to concatenate frequency (TRUE: mean, FALSE: sum)
scaleRange	point size scaling
ovlThresh	show text with this number of overlap between graphs
returnNet	return only the network (ig)
colPal	color palette to be used in RColorBrewer
colorText	whether to color text based on category
community	compare based on community (igraph), override tag
returnClass	return biotext class object, default to TRUE

Details

The function accepts list (named) of biotext object, and plot the merged network highlighting the intersection of the network and identified clusters.

Value

plot comparing gene clusters

Examples

net1 <- refseq(c("DDX41","IRF3","ERCC1","ERCC2","XRCC1"), plotType="network")
net2 <- refseq(c("DDX41","PNKP","ERCC3","IRF3","COPA"), plotType="network")
compare <- compareWordNet(list(net1, net2))

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.