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Last data update: 2014.03.03

R: To compare enriched functional annotations found by using...

BBplot

R Documentation

To compare enriched functional annotations found by using DAVID webservice.

Description

It uses a list of DAVIDFunctionalAnnotationChart objects to build a chart that shows how the functional annotations found by DAVID have changed across different experimental conditions. BBplot function can work with any kind of gene list and not only with up/down regulated gene lists.

Usage

BBplot(list.david.obj, max.pval = 0.01, min.ngenes = 5, max.ngenes = 500, 
       adj.method = "Benjamini", title = "BBplot", name.com = "***", 
       labels = c("down", "up"), colors = c("#009E73", "red"), print.term = "full")

Arguments

`list.david.obj`	(Required). List of 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) requested for each enriched annotations. Default values is 5.
`max.ngenes`	(Optional). Integer with the maximum number of genes (greater or equal) requested for each enriched annotations. Default values is 5.
`adj.method`	(Optional). Character with the name of the adjustment method. Default valuse is "Benjamini". Methods that are available: "Benjamini", "Bonferroni" or "FDR". It can be empty "".
`title`	(Optional). Character with the name of the buble plot. Default valuse is "Bubble plot".
`name.com`	(Optional). Character vector indicating the experimental conditions.
`labels`	(Optional). Character vector to specify the name used to indicate the down- and up-regulated gene lists. The default value is c("down", "up").
`colors`	(Optional). Character vector to specify the colors used to distinguish down- and up-regulated gene lists. The default value is c("#009E73", "red").
`print.term`	(Optional). Character vector to specify the term used to indicate the annotation: 'full', 'name' or 'description'. The default value is "full".

Details

The list of DAVIDFunctionalAnnotationChart objects should be generated by using the function DAVIDsearch.

Value

Return a ggplot2 graph.

Note

For each condition, provide two DAVIDFunctionalAnnotationChart objects: one for the up-regulated genes and other for the down-regulated genes.

Author(s)

Vittorio Fortino

Examples

  data(result.kegg)

  bbplot.kegg <- BBplot(result.kegg, max.pval = 0.05, min.ngenes = 10, 
                    name.com = c("Cond.1_12h","Cond.1_24h","Cond.2_12h","Cond.2_24h"), 
                    labels = c("down", "up"), colors = c("#009E73", "red"), 
                    title = "BBplot - KEGG", print.term = "full")
  bbplot.kegg
  ##ggsave("KEGG_terms.tiff", width=6, height=4, scale=2, dpi=200)

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/BBplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BBplot
> ### Title: To compare enriched functional annotations found by using DAVID
> ###   webservice.
> ### Aliases: BBplot
> 
> ### ** Examples
> 
>   data(result.kegg)
> 
>   bbplot.kegg <- BBplot(result.kegg, max.pval = 0.05, min.ngenes = 10, 
+                     name.com = c("Cond.1_12h","Cond.1_24h","Cond.2_12h","Cond.2_24h"), 
+                     labels = c("down", "up"), colors = c("#009E73", "red"), 
+                     title = "BBplot - KEGG", print.term = "full")
>   bbplot.kegg
>   ##ggsave("KEGG_terms.tiff", width=6, height=4, scale=2, dpi=200)
>   
>  
> 
> 
> 
> 
> dev.off()
null device 
          1 
>