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Last data update: 2014.03.03

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

Jplot

R Documentation

To compute and visualize Jaccard similarity score between two enrichment analysis results.

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

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BACA)

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BACA/Jplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Jplot
> ### Title: To compute and visualize Jaccard similarity score between two
> ###   enrichment analysis results.
> ### Aliases: Jplot
> 
> ### ** Examples
> 
>   data(result.kegg)
>   jplot.kegg <- Jplot(result.kegg[[4]], result.kegg[[2]], max.pval = 0.05, min.ngenes = 10) 
>   jplot.kegg
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>