# organism input possible:
### ARABIDOPSIS_THALIANA
### SACCHAROMYCES_CEREVISIAE
### CAENORHABDITIS_ELEGANS
### DROSOPHILA_MELANOGASTER
### DANIO_RERIO
### HOMO_SAPIENS (default)
### MUS_MUSCULUS
### RATTUS_NORVEGICUS
# runmodes input possible:
### mhg (single ranked list of genes)
### hg (target and background gene lists)
# ontologies input possible:
### proc (process)
### func (function)
### comp (component)
### all
# includeDups, revigo, fast input possible:
### 0 (false)
### 1 (true)
GOrilla <- function (targetFiles, backgroundFiles=NULL, outputDir=NULL, organism="HOMO_SAPIENS",runMode="mhg",ontology="all",pValue=0.01,name=NULL,email=NULL,includeDups=0,revigo=1,fast=1, scpPath=NULL, threads=getOption("threads",1L) ){
scriptURL="http://www.veralab.org/kkyle/automateGOrilla.pl"
l=list.files("~",pattern="automateGOrilla.pl",recursive=T)
if(length(l)==0){
cat("\nScript not found! Downloading...\n\n")
l="./automateGOrilla.pl"
download.file(scriptURL,destfile=l,method="wget")
}
else
l=paste0("~/",l)
if(is.null(outputDir))
outputDir="."
cmdString=paste("perl", l[1], "-targets", targetFiles, "-outputdir", outputDir)
if(!is.null(backgroundFiles))
cmdString=paste(cmdString, "-background", backgroundFiles)
cmdString=paste(cmdString,"-organism",organism,"-runmode",runMode,"-ontology",ontology,"-pvalue",pValue,"-includedups",includeDups,"-revigo",revigo,"-fast",fast)
if(!is.null(name))
cmdString=paste(cmdString,"-name",name)
if(!is.null(email))
cmdString=paste(cmdString,"-email",email)
print(cmdString)
cmdRun(cmdString,threads)
if(!is.null(scpPath))
cmdString=paste("scp -r",outputDir,scpPath)
cmdRun(cmdString,threads)
}
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