plot.CoDiNA {CoDiNA}

plot.CoDiNA

Description

Categorize the Nodes into Phi and groups categories. Also, creates an interactive view of the CoDiNA network.

Usage

## S3 method for class 'CoDiNA'
plot(
  x,
  cutoff.external = 0,
  cutoff.internal = 1,
  cutoff.ratio = 1,
  layout = NULL,
  smooth.edges = TRUE,
  path = NULL,
  MakeGroups = FALSE,
  Cluster = FALSE,
  legend = TRUE,
  manipulation = FALSE,
  sort.by.Phi = FALSE,
  ...
)

Arguments

x

Output from MakeDiffNet

cutoff.external

The cut-off between the clusters (delta from the center to the edge coordinates), the closer to 1, the better.

cutoff.internal

The cut-off inside the clusters (delta from the theoretical cluster to the edge coordinates), the closer to zero, the better.

cutoff.ratio

The cut-off for the ratio of both scores. Default is set to 1. The greater, the better.

layout

a layout from the igraph package.

smooth.edges

If the edges should be smoothed or not.

path

If the graph should be saved specify the name of the file.

MakeGroups

algorithm to find clusters. One of the followings: walktrap, optimal, spinglass, edge.betweenness, fast_greedy, infomap, louvain, label_prop, leading_eigen. Default to FALSE.

Cluster

TRUE or FALSE if the nodes should be clustered (double click to uncluster).

legend

TRUE or FALSE if the legend should appear.

manipulation

TRUE or FALSE if the graph should be editable.

sort.by.Phi

if the graph should be plotted in the Phi order

...

Additional plotting parameters.

Value

Returns a list contatining: The nodes description, the Edges description and the network graph.

Author(s)

Deisy Morselli Gysi <deisy at bioinf.uni-leipzig.de>

Examples

suppressWarnings(RNGversion("3.5.0"))

Nodes = LETTERS[1:10]
Net1 = data.frame(Node.1 = sample(Nodes) , Node.2 = sample(Nodes), wTO = runif(10,-1,1))
Net2 = data.frame(Node.1 = sample(Nodes) , Node.2 = sample(Nodes), wTO = runif(10,-1,1))
Net3 = data.frame(Node.1 = sample(Nodes) , Node.2 = sample(Nodes), wTO = runif(10,-1,1))
DiffNet = MakeDiffNet (Data = list(Net1,Net2,Net3), Code = c('Net1', 'Net2', 'Net3') )
Graph = plot(x = DiffNet,
 layout = NULL, smooth.edges = TRUE,
 path = NULL, MakeGroups = FALSE, Cluster = FALSE,
 legend = TRUE, manipulation = FALSE, sort.by.Phi = FALSE)
Graph