DrInsight (version 0.1.2)

network.graph: Plot Drug and Pathway Interaction Network

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

# NOT RUN {
## 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)
# }