Plot region-gene associations

Plot region-gene associations

# S4 method for GreatJob
plotRegionGeneAssociations(object, ontology = NULL, term_id = NULL, which_plot = 1:3,
    request_interval = 10, max_tries = 100, verbose = great_opt$verbose)

Arguments

object

A GreatJob-class object returned by submitGreatJob.

ontology

A single ontology names. Valid values are in availableOntologies.

term_id

Term id in the selected ontology

which_plot

Which plots to draw? The value should be in 1, 2, 3. See "Details" section for explanation.

request_interval

Time interval for two requests. Default is 300 seconds.

max_tries

Maximal times for automatically reconnecting GREAT web server.

verbose

Whether to show messages.

Details

There are following figures:

  • Association between regions and genes (which_plot = 1).

  • Distribution of distance to TSS (which_plot = 2).

  • Distribution of absolute distance to TSS (which_plot = 3).

If ontology and term_id 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 term_id is from 'id' column in the table which is returned by getEnrichmentTables.

Author

Zuguang gu <z.gu@dkfz.de>

Examples

job = readRDS(system.file("extdata", "GreatJob.rds", package = "rGREAT"))

plotRegionGeneAssociations(job)

plotRegionGeneAssociations(job, which_plot = 1)

# Do not use other term_id for this example, or you need to generate a new `job` object.
plotRegionGeneAssociations(job, ontology = "GO Molecular Function",
    term_id = "GO:0004984")
#> The webpage for 'GO Molecular Function:GO:0004984' is available at:
#>   http://great.stanford.edu/public-4.0.4/cgi-bin/showTermDetails.php?termId=GO:0004984&ontoName=GOMolecularFunction&ontoUiName=GO Molecular Function&sessionName=20230401-public-4.0.4-Amwjvn&species=&foreName=fileba3c45b28db3.gz&backName=&table=region
#>  Note the web page might be deleted from GREAT web server because it is only for temporary use.