In brucosper/RadialGO: A Radial Tree Visualization of Gene Ontology Enrichment

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(radialgo)
install.packages("BiocManager", repos="http://cran.utstat.utoronto.ca/")
library(BiocManager)
BiocManager::install("topGO")
BiocManager::install("hgu95av2.db")
BiocManager::install("ALL")
library(topGO)
library(ALL)

Introduction

RadialGO is a package for visualizing Gene Ontology enrichment analyses, using a radial tree layout. This document gives a quick tour of how to use the package.

GO Enrichment

The function generateGraph() produces a graph of the GO enrichment, taking as input 3 parameters: the first is a CSV file containing a "GO ID" column, which consists of Gene Ontology identifiers such as "GO:0008150", and a "P value" column, consisting of the corresponding P-value in the enrichment analysis.

An example workflow follows.

Example

For this example we will obtain the GO enrichment results using the topGO package.

data(ALL)
data(geneList)
affyLib <- paste(annotation(ALL), "db", sep = ".")
library(package = affyLib, character.only = TRUE)
sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "BP",
                    allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10, 
                    annot = annFUN.db, affyLib = affyLib)
resultFisher <- runTest(sampleGOdata, algorithm = "classic", statistic = "fisher")

This gets us our GO enrichment analysis results in the variable resultFisher. We can use the score() function to extract a named numeric vector containing GO IDs and P values, which we will use to build a data frame.

df <- data.frame("GO ID"= names(score(resultFisher)), "P value"= as.numeric(score(resultFisher)))
df

We can store this data frame easily using the following code:

write.csv(df, "enrichment_results.csv")

Once we have this data frame, we can call generateGraph() to create our graph, and then render it:

library(radialgo)
library(DiagrammeR)
gr <- generateGraph(df, 5, 0.5)
DiagrammeR::grViz(generate_dot(gr))

brucosper/RadialGO documentation built on Dec. 8, 2019, 10:32 a.m.