Jplot: To compute and visualize Jaccard similarity score between two...

In BACA: Bubble Chart to Compare Biological Annotations by using DAVID

Description

Comparing two enrichment analysis results, it reveals the relationships existings between annotations found by using two different gene lists. The Jplot() function takes in input two different DAVIDFunctionalAnnotationChart objects (1 and 2) and provides in output a table/matrix with colored boxes. Each box reports the Jaccard index-based similarity score computed between the gene sets enriching two functional annotations.

Usage

Jplot(david.obj.1, david.obj.2,  max.pval = 0.01, min.ngenes = 5, title = "Jplot", 
       print.term ="full")

Arguments

david.obj.1	(Required). First DAVIDFunctionalAnnotationChart objects.
david.obj.2	(Required). Second DAVIDFunctionalAnnotationChart objects.
max.pval	(Optional). Numeric with the p-value that must be present in order to select the most significant enriched annotations. Default values is 0.01.
min.ngenes	(Optional). Integer with the minimum number of genes (greater or equal) that must be present in an enriched annotations. Default values is 5.
title	(Optional). Character with the name of the plot. Default valuse is "Bubble plot".
print.term	(Optional). Character vector to specify the term used to indicate the annotation: 'full', 'name' or 'description'. The default value is "full".

Value

Return a ggplot2 graph.

Note

The two DAVIDFunctionalAnnotationChart objects should be associated to two different enrichment analysis results.

Author(s)

Vittorio Fortino

See Also

DAVIDsearch BBplot

Examples

  data(result.kegg)
  jplot.kegg <- Jplot(result.kegg[[4]], result.kegg[[2]], max.pval = 0.05, min.ngenes = 10) 
  jplot.kegg

Example output

BACA documentation built on May 2, 2019, 7:41 a.m.