plot_change: Plotting the change in pathways order

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

Description

Function for plotting a lines plot of the difference in pathways' order. The resultant plot shows the comparison between the order of the original pathways and the order of the augmented pathways. It also contains a line with the order difference (order of the augmented pathways minus order of the original pathways). The order of a biological pathway is the number of genes that are involved in it.

Usage

plot_change(original_pathways, augmented_pathways, pathway_names, ...)

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>'.
...	Other arguments for the '<plotLines>' function.

Value

A lines plot of the comparison of pathways order.

Author(s)

Diana Diaz <dmd at wayne dot edu>

Examples

data(augmented_pathways)
data(kegg_pathways)
data(names_pathways)
plot_change(kegg_pathways,augmented_pathways, names_pathways)

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