pathways2pdf {mirIntegrator} | R Documentation |
This function creates a pdf file with plottings of a list of augmented pathways.
pathways2pdf(original_pathways, augmented_pathways, pathway_names, file)
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. |
A pdf file with the plottings of the augmented pathways.
Diana Diaz <dmd at wayne dot edu>
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")