visualize_011: 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 genomic context. LncRNAs are linked to the proteins that are products of their genomic context.

Usage

visualize_011(
  lncgenes,
  genomic_context,
  ensp_to_ensg,
  input_proteins,
  network_seeds,
  ppi_network,
  expanded_elements,
  mart,
  mart_symbol_column = NULL
)

Arguments

lncgenes	a list of lncRNA genes
genomic_context	the genomc context of the lncRNAs (see get_genomic_context)
ensp_to_ensg	a two column data.frame for mapping proteins to their producer genes (see also get_stringdb )
input_proteins	the complete list of input proteins,that are of interest for the study
network_seeds	the lsit of seed protieins
ppi_network	a two column data.frame representing PPI network edges (see also get_stringdb )
expanded_elements	the list of proteins that must be visualized
mart	a biomaRt ojbect used to visualize symbols instead of Ensembl IDs
mart_symbol_column	column of the biomaRt ojbect fomr wich symbols are retrieved

Value

visualizes the network in the Viewer window

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