plotPairwise {CompGO} | R Documentation |
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.
plotPairwise(setA, setB, cutoff = NULL, useRawPvals = FALSE, plotNA = TRUE, model = "lm", ontology = NULL)
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 |
data(funChart1) data(funChart2) plotPairwise(funChart1, funChart2)