plotRegionGeneAssociationGraphs-GreatJob-method: Plot region-gene association figures
In rGREAT: Client for GREAT Analysis

Description Usage Arguments Details Value Author(s) Examples

Plot region-gene association figures

## S4 method for signature 'GreatJob'
plotRegionGeneAssociationGraphs(job, type = 1:3, ontology = NULL,
    termID = NULL, request_interval = 10, max_tries = 100, verbose = TRUE,
    plot = TRUE)

`job`	a `GreatJob-class` instance
`type`	type of plots, should be in `1, 2, 3`. See details section for explanation
`ontology`	ontology name
`termID`	term id which corresponds to the selected ontology
`request_interval`	time interval for two requests. Default is 300 seconds.
`max_tries`	maximum tries
`verbose`	whether show message
`plot`	whether make plots

Generated figures are:

association between regions and genes
distribution of distance to TSS
distribution of absolute distance to TSS

If ontology and termID are set, only regions and genes corresponding to selected ontology term will be used. Valid value for ontology is in availableOntologies and valid value for termID is from 'id' column in the table which is returned by getEnrichmentTables.

a GRanges object. Columns in metadata are:

gene: genes that are associated with corresponding regions
distTSS: distance from the regions to TSS of the associated gene

The returned values corresponds to whole input regions or only regions in specified ontology term, depending on user's setting.

If there is no gene associated with the region, corresponding gene and distTSS columns will be NA.

Zuguang gu <z.gu@dkfz.de>

# note the `job` was generated from GREAT 3.0.0
job = readRDS(system.file("extdata", "job.rds", package = "rGREAT"))

res = plotRegionGeneAssociationGraphs(job)
res

plotRegionGeneAssociationGraphs(job, type = 1)

res = plotRegionGeneAssociationGraphs(job, ontology = "GO Molecular Function",
    termID = "GO:0004984")
res