Description Usage Arguments Examples

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.

1 2 | ```
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 |

1 2 3 | ```
data(funChart1)
data(funChart2)
plotPairwise(funChart1, funChart2)
``` |

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