NetVis: NetVis

In deisygysi/wTO: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network

NetVis

Description

Given a set of Nodes and the weight of the edges, a cutoff for the edges, it draws the networks. Returns a list with the nodes and edges attributes. And plots the network.

Usage

NetVis(
  Node.1,
  Node.2,
  wTO,
  pval = NULL,
  MakeGroups = FALSE,
  padj = NULL,
  cutoff = list(kind = "Threshold", value = 0.5),
  layout = NULL,
  smooth.edges = T,
  path = NULL,
  Cluster = F,
  legend = T,
  shape = list(shape = "triangle", names = NULL),
  manipulation = F
)

Arguments

Node.1	Names of the Nodes.1 that are connected to the Nodes.2. It's the output from wTO.Complete or Consensus.
Node.2	Names of the Nodes.2 that are connected to the Nodes.1. It's the output from wTO.Complete or Consensus.
wTO	weight of the links, the wTO output from wTO.Complete or wTO.Consensus.
pval	p-values for the wTO value. By default it is NULL.
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.
padj	Adjusted p-values for the wTO value. By default it is NULL.
cutoff	It's a list containing the kind of cutoff to be used (pval, Threshold or pval.adj)and it's value. Example: cutoff= list(kind = "Threshold", value = 0.5)
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.
Cluster	TRUE or FALSE if the nodes should be clustered (double click to uncluster).
legend	TRUE or FALSE if the legend should appear.
shape	a list shape=list(shape = "triangle", names = NULL), with the shape and the IDs that should have a different shape, shape can be: diamond, star, triangle, triangleDown or square.
manipulation	TRUE or FALSE if the graph should be editable.

Author(s)

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

Examples

 X =  wTO.Complete( k =1, n = 5, Data = Microarray_Expression1,
 Overlap = ExampleGRF$x, method = "p",  plot = FALSE)
# Plot with the default aguments.
 NetVis(Node.1 = X$wTO$Node.1, Node.2 = X$wTO$Node.2,
 wTO = X$wTO$wTO_sign, cutoff = list(kind =
"Threshold", value = 0.50))

## Not run: 
# Plotting just the edges with p-value < 0.05, with straight edges, nodes clustered,
# no legend and mapipulation of the graph enabled.
  NetVis(Node.1 = X$wTO$Node.1, Node.2 = X$wTO$Node.2,
 wTO = X$wTO$wTO_sign, pval = X$wTO$pval_sign,
 padj = X$wTO$pval_sign,
  cutoff= list(kind = "pval", value = 0.05),
  smooth.edges = FALSE,
 Cluster = TRUE, legend = FALSE, manipulation = TRUE)
# Plotting just the edges with wTO > 0.50, no legend and the nodes:
# "ZNF738", "ZNF677" with triagle shape,
# no legend and mapipulation of the graph enabled.
 NetVis(Node.1 = X$wTO$Node.1, Node.2 = X$wTO$Node.2,
 wTO = X$wTO$wTO_sign, pval = X$wTO$pval_sign,
 padj = X$wTO$pval_sign, cutoff= list(kind = "Threshold", value = 0.5),legend = FALSE,
 shape = list(shape = "triangle", names = c("ZNF738", "ZNF677")))

 
## End(Not run)

deisygysi/wTO documentation built on May 25, 2022, 2:46 a.m.