plotWordFreq {geneXtendeR} | R Documentation

## Plots word frequencies found within gene ontology terms

### Description

Creates barplots of word frequencies from gene ontology terms derived from either biological process (BP), cellular compartment (CC), or molecular function (MF) of genes-under-peaks that are unique between two different upstream extension levels.

### Usage

    plotWordFreq(organism, start, end, GOcategory, GOspecies, word_count)

### Arguments

`organism` | Object name assigned from readGFF() command.
`start` | Lower bound of upstream extension.
`end` | Upper bound of upstream extension.
`GOcategory` | Either BP, CC, or MF.
`GOspecies` | Either org.Ag.eg.db (mosquito), org.Bt.eg.db (bovine), org.Ce.eg.db (worm), org.Cf.eg.db (canine), org.Dm.eg.db (fly), org.Dr.eg.db (zebrafish), org.Gg.eg.db (chicken), org.Hs.eg.db (human), org.Mm.eg.db (mouse), org.Mmu.eg.db (rhesus), org.Pt.eg.db (chimpanzee), org.Rn.eg.db (rat), org.Sc.sgd.db (yeast), org.Ss.eg.db (pig), or org.Xl.eg.db (frog).
`word_count` | Number of top words to display

### Value

A barplot comprised of words sorted by frequency of occurrence from gene ontology terms of either a BP, CC, or MF category.

### Examples

    library(rtracklayer)
    rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz")
    fpath <- system.file("extdata", "somepeaksfile.txt", package="geneXtendeR")
    peaksInput(fpath)
    library(tm)
    library(SnowballC)
    library(wordcloud)
    library(RColorBrewer)
    library(org.Rn.eg.db)
    plotWordFreq(rat, 0, 500, BP, org.Rn.eg.db, 10)

[Package geneXtendeR version 1.13.0 Index]