getPathwayIgraph: getPathwayIgraph
In NCBI-Hackathons/Metabolomics-Data-Portal: Metabolomics Data Portal

Description Usage Arguments Value Examples

getPathwayIgraph

1	getPathwayIgraph(input, Pathway.Name, pmap.path = "./extdata")

`input`	- A list object of parameters (esp. from R shiny app). Required parameters are ptIDs, diagClass and pathwayMapId.
`Pathway.Name`	- The name of the pathway map for which you want the topological information.

template.ig - Igraph object of selected pathway map.

 data(Miller2015_Heparin)
# Input is supplied by R shiny app, but you can hard code parameters as a list object, too, to test functionality.
input = list()
input$ptIDs = colnames(Miller2015_Heparin)[4]
input$diagClass = "paa"
input$pathwayMapId = "All"
ig = getPathwayIgraph(input, Miller2015_Heparin)
# Returns a blank template for selected pathway.
plot.igraph(ig, edge.arrow.size = 0.01)