makeWordCloud: Makes word cloud from gene ontology terms

Description Usage Arguments Value Examples

View source: R/makeWordCloud.r

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

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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

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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)

geneXtendeR documentation built on Nov. 1, 2018, 3:34 a.m.