makeWordCloud {geneXtendeR} | R Documentation

## Makes word cloud from gene ontology terms

### Description

Creates word cloud 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

    makeWordCloud(organism, start, end, GOcategory, GOspecies)

### 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).

### Value

A word cloud comprised of words gathered 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)
    makeWordCloud(rat, 0, 500, BP, org.Rn.eg.db)

[Package geneXtendeR version 1.10.0 Index]