getPathwayMap: Get Pathway Map: Generate pathway map with patient data...

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

Description

Get Pathway Map: Generate pathway map with patient data superimposed.

Usage

getPathwayMap(input, zscore.data)

Arguments

input	- List of parameters passed from R shiny from UI. Important parameters will be input$ptIDs, input$pathwayMapId, and input$scalingFactor.
zscore.data	- A named vector of metabolites with corresponding z-scores.

Value

An SVG image of the selected pathway map in input$pathwayMapId, with the mean profile of input$ptIDs superimposed.

Examples

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$pathwayMapId = "allPathways"
input$scalingFactor = 1
svg_img = getPathwayMap(input, Miller2015_Heparin)
# SVG file will be saved at following path
svg_img$src
# Colorbar can be visualized this way
plot(svg_img$colorbar)

NCBI-Hackathons/Metabolomics-Data-Portal documentation built on May 31, 2019, 9:59 a.m.