plot_overlap: Plot a reconstructed network in comparison with a prior...

Description Usage Arguments Value Author(s) Examples

Description

Display a reconstructed network together with the provided prior network in the same plot.

Usage

1
2
3
   plot_overlap(adjcore, adjX, overlap, symbols.plot, ig.layout, main, nameA, nameB, 
                node.size1=25, node.size2=7, stimnodes=NULL, customtitle=NULL,
                col_equal="black", col_new="blue", col_missing="red", vlabel.cex=1)

Arguments

adjcore

Adjacency matrix of the prior network (row target activates column target, 0: no edge, 1: activation, 2: inhibition).

adjX

Adjacency matrix of the reconstructed consensus network (row target activates column target, 0: no edge, 1: activation, 2: inhibition).

overlap

Targets of prior and reconstructed network, i.e. row/column names of the adjacency matrices.

symbols.plot

Vertex label, i.e. row/column names of the adjacency matrices.

ig.layout

Layout matrix defining the positions of vertices in the plot. The row names are the targets and the column names are "x"" and "y"" as coordinates. The entries are numeric values.

main

Plot subtitle.

nameA

Provide a name for the prior network, e.g. "Prior".

nameB

Provide a name for the reconstructed network, e.g. "Reconstruction".

node.size1

Node size parameter.

node.size2

Node size parameter.

stimnodes

Vector of stimuli names.

customtitle

Plot title.

col_equal

Colour for common edge in prior and reconstructed network.

col_new

Colour for newly inferred edge in reconstructed network compared to prior.

col_missing

Colour for deleted edge in reconstructed network compared to prior.

vlabel.cex

Label size parameter.

Value

Plot of a reconstructed network in comparison with a prior network.

Author(s)

Christian Bender

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
	library(ddepn)
  ## simulate a network with 6 nodes and 2 distinct input stimuli
  set.seed(12345)
  signet <- signalnetwork(n=6, nstim=2, cstim=0, prop.inh=0.2)
  ## prior net
  prior <- signet$phi
  prior[5,3] <-  prior[2,1] <- 1
  prior[6,4] <- 0
  ## layout
  layoutMatrix<-matrix(0,nrow=6,ncol=2)
  rownames(layoutMatrix)<-rownames(prior)
  colnames(layoutMatrix)<-c("x","y")
  layoutMatrix[,"x"]<-rep(c(100,200),3)
  layoutMatrix[,"y"]<-c(100,100,200,200,300,300)
	plot_overlap(adjcore=prior, adjX=signet$phi, ig.layout=layoutMatrix,overlap=rownames(prior), nameA="Prior", nameB="Reconstruction", main="Test", symbols.plot=rownames(prior), stimnodes=names(unlist(signet$stimuli)))

ddepn documentation built on May 2, 2019, 4:42 p.m.