plotTwoGODags: Plots a directed acyclic graph of GO terms from two different...

In sam-bassett/CompGO: An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

Description

Plots a directed acyclic graph of GO terms from two different sources, using colour to show intersection and difference. This is useful to see the specific functional differences between gene lists, complementing the overall metric of gene list similarity

Usage

plotTwoGODags(setA, setB, ont = "BP", cutoff = 0.01, maxLabel = NULL,
  fullNames = TRUE, Pvalues = TRUE)

Arguments

setA	A DAVIDFunctionalAnnotationChart object
setB	A DAVIDFunctionalAnnotationChart object
ont	The ontology to use, one of BP, MF and CC
maxLabel	Maximum length of GO term to print
cutoff	The PValue cutoff to use
fullNames	Whether to print the full GO term label or just the GO id
Pvalues	Whether to print P-values alongside each label

References

Fresno, C. and Fernandes, E. (2013) RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API. http://david.abcc.ncifcrf.gov/

Examples

data(funChart1)
data(funChart2)
plotTwoGODags(funChart1, funChart2)

sam-bassett/CompGO documentation built on May 29, 2019, 1:01 p.m.