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create IGV viewer batch script (single range, as many tracks as you like)

createIgvBatchscript.Rd

this will create a batch script that may be run with the igv browser. An example command is given in the examples below. See the extern data for an example of what one of these scripts looks like.

Usage

createIgvBatchscript(
  bam_list,
  granges,
  igv_genome,
  output_dir,
  output_file_basename,
  exit_browser = TRUE,
  maxPanelHeight = 500
)

Arguments

bam_list

list of bamfiles -- multiple files means multiple tracks

granges

granges describing the range you wish to visualize -- range must be on one chromosome/contig

igv_genome

.genome file created by IGV tools

output_dir

where to deposit both the script and the browser shots

output_file_basename

this will serve as both the name of the browser shot after running IGV, and the name o the batchscript itself

exit_browser

Default is TRUE, which means that the batchscript will be written in a way that the browser will take an image, save it, and exit. Set to false and this script may be used to launch an interactive session.

maxPanelHeight

default 500. height of the IGV window

Value

None. This prints a batch script to the output dir

Note

run on the command line like so xvfb-run --auto-servernum igv.sh -b script.bat