CompGO (version 1.8.1)

plotPairwise: Generates a scatterplot of two sets of GO terms based on DAVID P-values

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)