CorrelationNetwork-class: Correlation Network
In VEuPathDB/plot.data: Create `data.table`s of Ready to Plot Data

CorrelationNetwork-class

R Documentation

Correlation Network

Description

A class for representing networks of pairwise correlations. A network is composed of nodes and links (edges, connections, etc.). A link is represented as a pair of nodes, with attributes such as correlationCoef and pValue (see Link). To represent a network, we need both the list of links in the network and a list of nodes in case some nodes have no links. A network can also have properties such as directedness, levels, colors, etc. (coming soon).

Slots

links: CorrelationLinkList object defining the links in the network.
nodes: NodeList object defining the nodes in the network. Some nodes may not have any links.
linkColorScheme: string defining the type of coloring scheme the links follow. Options are 'none' (default) and 'posneg'. In the case of 'posneg', the links color slot will be set to 1 if the link is positive, and -1 if the link is negative. Use a method assignLinkColors() to assign colors to links and set this slot's value.
variableMapping: veupathUtils::VariableMetadataList object defining the variable mappings in the network.
correlationCoefThreshold: numeric defining the correlation coefficient threshold for filtering links. Default is NA (no filtering). Any link with an absolute correlation coefficient below this threshold will be filtered out.
pValueThreshold: numeric defining the p-value threshold for filtering links. Default is NA (no filtering). Any link with an p-value above this threshold will be filtered out.