## ----, echo = FALSE, message = FALSE-------------------------------------
library(knitr)
knitr::opts_chunk$set(
    error = FALSE,
    tidy  = FALSE,
    message = FALSE,
    fig.align = "center")
options(width = 100)
options(markdown.HTML.stylesheet = "custom.css")


## ----, echo = 2----------------------------------------------------------
suppressWarnings(suppressPackageStartupMessages(library(rGREAT)))
library(rGREAT)


## ------------------------------------------------------------------------
set.seed(123)
bed = circlize::generateRandomBed(nr = 1000, nc = 0)
head(bed)


## ------------------------------------------------------------------------
job = submitGreatJob(bed)


## ------------------------------------------------------------------------
job


## ----, eval = FALSE------------------------------------------------------
## job = submitGreatJob(bed, species = "mm9")
## job = submitGreatJob(bed, bg, species = "mm9", bgChoise = "data")
## job = submitGreatJob(bed, adv_upstream = 10, adv_downstream = 2, adv_span = 2000)
## job = submitGreatJob(bed, rule = "twoClosest", adv_twoDistance = 2000)
## job = submitGreatJob(bed, rule = "oneClosest", adv_oneDistance = 2000)


## ------------------------------------------------------------------------
tb = getEnrichmentTables(job)
names(tb)
head(tb[[1]])


## ------------------------------------------------------------------------
job


## ----, eval = FALSE------------------------------------------------------
## tb = getEnrichmentTables(job, ontology = c("GO Molecular Function", "BioCyc Pathway"))
## tb = getEnrichmentTables(job, category = c("GO"))


## ------------------------------------------------------------------------
availableOntologies(job)
availableCategories(job)
availableOntologies(job, category = "Pathway Data")


## ----, fig.width = 12, fig.height = 4, fig.align = 'center'--------------
par(mfrow = c(1, 3))
res = plotRegionGeneAssociationGraphs(job)
res


## ----, eval = FALSE------------------------------------------------------
## plotRegionGeneAssociationGraphs(job, type = 1)


## ----, fig.width = 12, fig.height = 4------------------------------------
par(mfrow = c(1, 3))
res = plotRegionGeneAssociationGraphs(job, ontology = "GO Molecular Function",
    termID = "GO:0004984")
res