mirIntegrator (version 1.2.0)

pathways2pdf: Export augmented pathways to pdf

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 ''. 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 ''. 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 ''.

file

The name of the file where the plots will be saved.

Value

A pdf file with the plottings of the augmented pathways.

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")