plotPairwise: Generates a scatterplot of two sets of GO terms based on...

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

Description

Generates a -log10 scatterplot of two sets of GO terms by p-value or corrected p-value with linear fit and correlation. Also includes a Jaccard metric for gene overlap within each GO term. Useful as an overall metric of gene list similarity. NOTE: The plotZScores function is more statistically sound, you should use that instead of this.

Usage

plotPairwise(setA, setB, cutoff = NULL, useRawPvals = FALSE,
  plotNA = TRUE, model = "lm", ontology = NULL)

Arguments

setA	DAVIDFunctionalAnnotationChart object to compare
setB	DAVIDFunctionalAnnotationChart object to compare
cutoff	The p-value or adjusted p-value to use as a cutoff
useRawPvals	If false, uses adjusted p-values, otherwise uses the raw ones
plotNA	If true, any GO term present in only one list is considered to have a p-value of 1 in the other; otherwise, it is simply removed
model	The model to use when plotting linear fit, default 'lm'
ontology	If a specific ontology (MF, BP, CC) is wanted rather than all terms, supply it here as a string

Examples

data(funChart1)
data(funChart2)
plotPairwise(funChart1, funChart2)

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