showInIGB: Change current view in IGB

Description Usage Arguments Details Value Note Note Author(s) References See Also Examples

View source: R/ViewInIGB.R

Description

Low level function to directly manipulate what is being shown in a running IGB session. It is safe for direct use but higher level interfaces are recommended.

Usage

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showInIGB(con, genome = NULL, goto = NULL, dataFile = NULL, loadMode, refresh = TRUE, select = NULL, sleep = NULL)

Arguments

con

A (socket) connection to a running IGB session.

genome

A character indicating the name of genome (including version) to be shown. Must be in a form IGB accepts, eg "H_sapiens_Feb_2009".

goto

A GRanges object indicating the viewing region desired or NULL for the default. Should contain one range with the name of the chromosome to view in the seqnames slot.

dataFile

A character containing the full path or URL to the data file to be loaded.

loadMode

Character value indicating how the data should be loaded. Must be one of "REGION_IN_VIEW", "WHOLE_CHROMOSOME", and "WHOLE_GENOME"

refresh

Logical indicating whether the view should be refreshed after loading the data. Defaults to TRUE.

select

A character vector indicating features to be selected.

sleep

Numeric value vindicating number of milliseconds IGB application should sleep, or NULL for no sleep.

Details

When this function is called, scripting instructions are sent to the specified IGB session via con

Value

The return value is not meaningful. When the function is called the effects should be immediately apparent in the running IGB session.

Note

An IGB session must already be running (and connected to by con) before this function is called.

Note

While the current genome will change immediately in the corresponding IGB session (if specified), data can take some time to load once the instruction has been sent.

Author(s)

Gabriel Becker

References

Vora, Hiral. "Scripting", IGB User's Guide, bioviz, Nov 1, 2011. http://wiki.transvar.org/confluence/display/igbman/Scripting

See Also

ViewInIGB

Examples

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## Not run: 
showInIGB(con = socket("localhost", "7085"), genome
="H_sapiens_Feb_2009", dataFile =
"http://netaffxdas.affymetrix.com/quickload_data/H_sapiens_Feb_2009/cytoBand.cyt",
loadmode = "REGION_IN_VIEW")

## End(Not run)

gmbecker/rigbLite documentation built on May 14, 2017, 12:57 p.m.