network.graph: Plot Drug and Pathway Interaction Network

In DrInsight: Drug Repurposing: Integration and Systematic Investigation of Genomic High Throughput Data

Description

This function allows user to plot the drug-pathway interaction network and returns the drug-pathway interaction contigency table.

Usage

network.graph(
  path.analysis.res = path.analysis.res,
  pathway.FDR.cutoff = 0.1,
  pathway.label = FALSE,
  drug.label.size = 1.2,
  path.label.size = 0.8,
  return.adj.table = TRUE
)

Arguments

path.analysis.res	The pathway analysis results. Output of function pathway.analysis().
pathway.FDR.cutoff	The FDR threshold to select significant drug specific pathways and the default is 0.1.
pathway.label	True or False specofying if show pathway labels in the graph.
drug.label.size	The number indicating the size of drug labels in the graph.
path.label.size	The number indicating the size of pathway labels in the graph.
return.adj.table	True or False specifying if return the resulted drug-pathway contigency table. In the returned table, 1's represent that the pathway is up-regulated by the drug; -1's reprensent down-regulation and 0's no-regulation.

Examples

## get the Dr. Insight drug identification results
drug.ident.res = drug.ident(query.data = example.disease, cmap.ref.profiles = example.drug.profiles,
                 repurposing.unit = "treatment", connectivity = "negative")

## load in example pathway data
data("example.pathway")

## Performe pathway analysis (for the drugs that are identified by ident.drug())
path.analysis.res = pathway.analysis(drug.ident.res = drug.ident.res,
                    pathway.list = example.pathway,drug.FDR.cutoff = 0.5)

drug.pathway.network = network.graph(path.analysis.res, pathway.FDR.cutoff = 0.5,
                       return.adj.table = TRUE, pathway.label = TRUE)

DrInsight documentation built on July 8, 2020, 7:36 p.m.