igv: igv

igvR 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

Author(s)

Marcin Imielinski


mskilab/skitools documentation built on July 5, 2024, 7:27 a.m.