plotNetwork: Plot correlation network map

In wenbostar/metaX: A flexible and comprehensive software for processing omics data.

Plot correlation network map

Description

Plot correlation network map

Usage

plotNetwork(para, group, valueID = "value", cor.thr = 0.95,
  degree.thr = 10, size.factor = 0.5, layout = layout_in_circle,
  showPlot = FALSE, graph_format = "gml", ...)

Arguments

para	A metaXpara object
group	Samples used for plot
valueID	The name of the column that used for plot
cor.thr	Threshold of correlation
degree.thr	Threshold of degree of node
size.factor	Node size factor for plot
layout	layout for plotting
showPlot	Whether or not to print the figure to screen
graph_format	The file format for graph data to save. Currently, "edgelist", "pajek", "ncol", "lgl", "graphml", "dimacs", "gml", "dot" and "leda" are supported.
...	Additional parameter

Value

An object of igraph

Author(s)

Bo Wen [e-mail]

Examples

para <- new("metaXpara")
pfile <- system.file("extdata/MTBLS79.txt",package = "metaX")
sfile <- system.file("extdata/MTBLS79_sampleList.txt",package = "metaX")
rawPeaks(para) <- read.delim(pfile,check.names = FALSE)
sampleListFile(para) <- sfile
para <- reSetPeaksData(para)
para <- missingValueImpute(para)
gg <- plotNetwork(para,group=c("S","C"),degree.thr = 10,cor.thr = 0.8)

wenbostar/metaX documentation built on July 4, 2023, 7:50 p.m.