visualize: Visualization of the expanded network

In InfOmics/LErNet: LErNet: characterization of lncRNAs via context-aware network expansion and enrichment analysis

Description

Visualizes the expanded network, composed by seed proteins and connectors. LncRNA are added together with extra edges in order to report the lncrna context. LncRNAs are linked to the proteins that are products of their lncrna context.

Usage

visualize(
  lncrna_context,
  de_proteins,
  network_seeds,
  expanded_elements,
  bg_ppi_network,
  labels
)

Arguments

lncrna_context	the genomic and interaction context of the lncRNAs (see get_genomic_context) and search_in_arenaidb
de_proteins	the complete vector of input proteins,that are of interest for the study
network_seeds	the list of seed proteins
expanded_elements	the list of proteins (see also expand_seeds ) that must be visualized
bg_ppi_network	a two column data.frame representing PPI network edges (see also get_stringdb )

Value

visualizes the network in the Viewer window

InfOmics/LErNet documentation built on April 10, 2021, 4:49 p.m.