compareWordNet: compareWordNet

View source: R/compareWordNet.R

compareWordNetR Documentation

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.