plot_augmented_pathway: Plotting of augmented pathway

In mirIntegrator: Integrating microRNA expression into signaling pathways for pathway analysis

Description

Functions for plotting a particular augmented pathway. In the plot, miRNAs that were added to the original pathway are differentiated from proteins that were originally in the pathway. Blue boxes represent the proteins that were part of the original pathway, and black boxes represent the miRNAs that were added during augmentation.

Usage

plot_augmented_pathway(original_pathway, augmented_pathway,
  pathway_name = " ", ...)

Arguments

original_pathway	A graph::graphNEL object where each of the nodes is named with '<gene_ID>'. Nodes of each graph::graphNEL represent the genes involved in the pathway and edges represent the biological interactions (activation or repression) among those genes.
augmented_pathway	A graph::graphNEL object where each of the nodes is named with '<gene_ID>'. Nodes of each graph::graphNEL represent genes and miRNAs involved in the pathway and edges represent the biological interactions (activation or repression) among them.
pathway_name	The name of the pathway.
...	Other arguments for the '<plotPathway2Colors>' function.

Value

A plot of one augmented pathway with the new nodes highlighted in black.

Author(s)

Diana Diaz <dmd at wayne dot edu>

Examples

data(augmented_pathways)
data(kegg_pathways)
data(names_pathways) 

plot_augmented_pathway(kegg_pathways[[18]], augmented_pathways[[18]],
                      pathway_name = names_pathways[[18]])

mirIntegrator documentation built on Nov. 8, 2020, 8:28 p.m.