plot a network based on a symmetric disease similarity matrix

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

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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

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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)

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