pathways2pdf: Export augmented pathways to pdf

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

Description

This function creates a pdf file with plottings of a list of augmented pathways.

Usage

pathways2pdf(original_pathways, augmented_pathways, pathway_names, file)

Arguments

original_pathways	A list of graph::graphNEL objects 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 (activation or repression).
augmented_pathways	A list of graph::graphNEL objects 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_names	A list of names of the pathways named by '<pathway_ID>'.
file	The name of the file where the plots will be saved.

Value

A pdf file with the plottings of the augmented pathways.

Author(s)

Diana Diaz <dmd at wayne dot edu>

Examples

data(augmented_pathways)
data(kegg_pathways)
data(names_pathways)
#The following instruction writes a pfd with three pathways
pathways2pdf(kegg_pathways[18:20],augmented_pathways[18:20],
             names_pathways[18:20], "three_pathways.pdf")
#The following instruction writes a pfd with all the pathways:
#NOTE: It may take time.
# pathways2pdf(kegg_pathways,augmented_pathways, 
#              names_pathways, "all_pathways.pdf")

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