igv: igv
In mskilab/skitools: Various mskilab R utilties

igv	R Documentation

igv

Description

Controls IGV on localhost (or specified host, separate from where R session is running). Igv application must be running and listening to a specified port. Then if you configure this port via environment variables (IGV_HOST, IGV_PORT) in the current R session then you can apply the following usages

igv(fn) ## sends any given file(s) into igv (eg .bam, .wig, .bed) igv(loci = cool.loci) ## plots the windows specified as GRanges or IGV-parsable strings (eg gene name) igv(gr = cool.gr) ## sends granges object to igv session, Note: currently requires the ability to write to a public_html that is web viewable by computer running IGV igv(snapshot = fn) ## sends current screen to file igv(new = TRUE) ## refreshes current session igv(reset = TRUE) ## resets connections, sometimes useful if IGV not responding

If alternate file paths are present on server (where R is runinng) and computer running IGV, then can specify gsub.paths variable which is a list of length 2 vectors specifying how to convert file paths from arguments given to igv to ones that can be loaded locally.

Usage

igv(
  paths = NULL,
  gr = NULL,
  loci = NULL,
  snapshot = NULL,
  track.view = NULL,
  new = FALSE,
  reset = FALSE,
  wkspace = "PanLungWGS",
  host = Sys.getenv("IGV_HOST"),
  mac = !grepl("(^cga)|(node\\d+)", host),
  rawpaths = FALSE,
  sort.locus = NULL,
  gsub.paths = list(),
  port = Sys.getenv("IGV_PORT")
)

Arguments

`paths`	file paths to display on current igv session (=NULL)
`gr`	GRanges or GRAngesList of numeric genomic data or interval genomic annotations to send to IGV session, if gr has field $score then data will be dumped to .bw otherwise to .bed or .gff (=NULL)
`loci`	GRanges or IGV parsable string specifying what window(s) on genome to view (=NULL)
`snapshot`	file path to store snapshot in (has to be interpretable on file system where IGV is running)
`track.view`	command for setting the track display mode ("expand","squish" or "collapse")
`new`	logical flag whether to start new IGV session
`reset`	logical flag whether to reset connection between R and IGV (useful if IGV non responsive)
`host`	character specifying host where IGV is running
`mac`	logical flag specifying whether host is a local "mac" (ie then apply gsub.paths) otherwise keep paths the same
`gsub.paths`	list of length 2 vectors specifying gsub args to apply to filenames when mac = TRUE
`port`	integer specifying port where IGV is running