regnet (version 1.0.2)

plot.regnet: plot a regnet object

Description

plot the network structures of the identified genetic variants.

Usage

# S3 method for regnet
plot(
  x,
  subnetworks = FALSE,
  vsize = 10,
  labelDist = 2,
  minVertices = 2,
  theta = 5,
  ...
)

Value

an object of class "igraph" is returned in default. When subnetworks=TRUE, a list of "igraph" objects (sub-networks) is returned.

Arguments

x

a regnet object.

subnetworks

whether to plot sub-networks

vsize

the size of the vertex

labelDist

the distance of the label from the center of the vertex.

minVertices

the minimum number of vertices a sub-network should contain.

theta

the multiplier for the width of the edge. Specifically, \(edge.width=\theta\times adjacency\). The default is 5.

...

other plot arguments

Details

This function depends on the "igraph" package in generating the network graphs. It returns a (list of) igraph object(s), on which users can do further modification on the network graphs.

See Also

regnet

Examples

# \donttest{
data(ContExample)
X = rgn.tcga$X
Y = rgn.tcga$Y
clv = (1:2)
fit = regnet(X, Y, "continuous", "network", rgn.tcga$lamb1, rgn.tcga$lamb2, clv =clv, alpha.i=0.5)

plot(fit)
plot(fit, subnetworks = TRUE, vsize=20, labelDist = 3, theta = 5)
# }