netgraph: Network connectivity plot

In bioinfo-ircm/aiMeRA: Modular Response Analysis for the quantitative analysis of connectivity in biological networks

Description

Plots a graphic representation of a biological network connectivity map calculated by MRA.

Usage

netgraph(map,layout=igraph::layout_with_kk,pertu=NULL,inter=NULL,
      cutoff=NULL,main=NULL,digits=2,outfile=NULL,module.in=NULL,
      module.out=NULL, no.module=NULL,neg.col="red",pos.col="green", ...)

Arguments

map	A list containing the connectivity map (link matrix) of a network, and local matrix responses to perturbations, i.e., the output of “'mra“'.
layout	Either a data.frame containing the x and y coordinates and the color of the vertices in the network, or a layout function according to the igraph package. Default uses the "layout_with_kk" igraph layout.
pertu	The name of perturbations to be plotted as vertices in the network.
inter	Confidence intervals calculated by “'interval“'; connectivity coefficient with a confidence interval that does not include 0 are deemed significant and marked by an asterisk.
cutoff	Minimum value for a connectivity link coefficient between two modules for being plotted.
main	A character string giving the title of the plot.
digits	Number of digits to be plotted for each connectivity coefficient.
outfile	Optional. A character string giving the name of the output file in graphML format.
module.in	The name of one or more nodes for which only the incoming connectivity from other nodes of the network should be plotted.
module.out	The name of one or more nodes for which only the outcoming connectivity to other nodes of the network should be plotted.
no.module	The name of one or more nodes for which incoming and outcoming connectivity should not be plotted.
neg.col	A color to be used for arrows with negative connectivity coefficients
pos.col	A color to be used for arrows with positive connectivity coefficients
...	Arguments to be passed to igraph plot such as vertex and edges plotting parameters.

Value

If layout is an igraph function then a data.frame containing the coordinates of the layout selected is returned. If outfile is not NULL, then the network is written in the graphML file format.

Examples

data=data.setup(list(estr1_A,estr1_B,estr2_A,estr2_B,estr3_A,estr3_B))
tec.av=list(data2sdmean(data[1:2])$mean,data2sdmean(data[3:4])$mean,data2sdmean(data[5:6])$mean)
data.mean=data2sdmean(tec.av)$mean
lb="E2"
data.rp=2*(data.mean[,colnames(data.mean)!=lb]-data.mean[,lb])/(data.mean[,colnames(data.mean)!=lb]+data.mean[,lb])
rules=c("E2+siLCoR->LCoR","E2+siRIP140->RIP140","Et->Luciferase","E2->0")
matp=read.rules(rules)
#The variance of each variable was estimated employing an estimator optimized for a
#small sample size from Statistical Process Control theory
#(Wheeler and Chambers, 1992; Harter, 1960). The standard deviation was computed for
#the global response matrices and stored into the sd.ex table which is included
#in the package)
inter=interval(data.rp,sd.tab=sd.ex,matp=matp,Rp=TRUE)
map=mra(data.rp,matp,Rp=TRUE,check=FALSE)
netgraph(map,inter=inter)

bioinfo-ircm/aiMeRA documentation built on Oct. 1, 2021, 8:11 a.m.