Skip to content

Latest commit

 

History

History
46 lines (36 loc) · 1.48 KB

README.md

File metadata and controls

46 lines (36 loc) · 1.48 KB
Raw

RadialGO

A radial tree visualization for Gene Ontology enrichment analysis

The goal of this package is to provide a visualization of GO enrichment analysis in a radial tree format.

Installation

You can install the latest version using

require("devtools")
install_github("brucosper/RadialGO", build_vignettes=TRUE)
library("radialgo")

To run the package use

radialgo()

Overview

The package takes a list of Gene Ontology IDs and their corresponding P-values, and takes the graph implied by the top nodes (i.e. gets their ancestors), removing the ancestors which have a corresponding P-value smaller than the user-specified cutoff. It then graphs these nodes, along with the edge relationships, and outputs it.

Contributions

The author of the package is Bruno Pereira. The functions available within this package include.

library("RadialGO")
lsf.str("package:RadialGO")
  • generateGraph

The generateGraph function was authored by Bruno Pereira, as well as the internal helper functions, which build the list of nodes implied by the input, as well as the edges. It uses the DiagrammeR package for generating graphical output. The GO.db and the AnnotationDbi packages were used to retrieve information about GO terms. The invert function in the searchable package was used for facilitating data retrieval from a named numerical vector. The shiny package was used to provide an interactive app for running the function.