plot_net {dSimer} | R Documentation

## 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

    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)

[Package dSimer version 1.6.0 Index]