plot_net: plot a network based on a symmetric disease similarity matrix

In PengNi/dSimer: Integration of Disease Similarity Methods

Description

plot a network/graph of a symmetric disease similarity matrix, note that a unsymmetric matrix can't be visualized into a network by this method.

Usage

plot_net(simmat, cutoff = 1, vertex.label.font = 2,
  vertex.label.dist = 0.5, vertex.label.color = "black",
  vertex.label.cex = 0.8, vertex.shape = "circle",
  vertex.color = "paleturquoise", vertex.size = 20, edge.color = "red",
  layout = layout.fruchterman.reingold)

Arguments

simmat	a symmetric similarity matrix
cutoff	a cutoff value, only disease pairs have similarity scores no less than cutoff will be visualized in the network
vertex.label.font	label text font
vertex.label.dist	label text dist
vertex.label.color	label text color
vertex.label.cex	label text cex
vertex.shape	vertex shape
vertex.color	vertex color
vertex.size	vertex size
edge.color	edge color
layout	layout

Value

an igraph plot object

Author(s)

Peng Ni, Min Li

Examples

data(d2g_separation)
data(interactome)

graph_interactome<-graph.data.frame(interactome,directed=FALSE)
ds<-c("myocardial ischemia","myocardial infarction","coronary artery disease",
 "cerebrovascular disorders","arthritis, rheumatoid","diabetes mellitus, type 1",
 "autoimmune diseases of the nervous system","demyelinating autoimmune diseases, cns",
 "respiratory hypersensitivity","asthma","retinitis pigmentosa",
 "retinal degeneration","macular degeneration")
 
sep<-Separation(ds,ds,d2g_separation,graph_interactome)
sim<-Separation2Similarity(sep)
plot_net(sim,cutoff=0.2)

PengNi/dSimer documentation built on May 8, 2019, 1:28 a.m.