plot.CoDiNA: plot.CoDiNA

In CoDiNA: Co-Expression Differential Network Analysis

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

CoDiNA documentation built on July 15, 2020, 5:07 p.m.