wTO (version 2.1)

NetVis: 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

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

Examples

if (FALSE) {
 X =  wTO.Complete( k =1, n = 5, Data = Microarray_Expression1,
 Overlap = ExampleGRF$x[1:10], method = "p",  plot = FALSE)
# Plot with the default aguments.
 NetVis(Node.1 = X$wTO$Node.1, Node.2 = X$wTO$Node.2,
 wTO = X$wTO$wTO_sign, cutoff = list(kind =
"Threshold", value = 0.50))

# 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")))

 }