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Export R script

The linear genome view's menu has an Export R script item. It downloads jbrowse_view.R, a short script that redraws the tracks open in the view, over the regions on screen, in R:

  • Each track is one call to ggjbrowse, which runs JBrowse's own data engine inside R and reads the track with the settings it has in the view.
  • The figure is one call, jbrowse_stack(), which stacks the tracks as the view does. source() the script and the figure appears; Rscript writes figure.png.
library(ggjbrowse)

locus <- "ctgA:1,001-9,000"

# GFF3Tabix genes
genes <- jbrowse_features("https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.sort.gff3.gz",
  locus,
  display = list(heightMode = "fit", height = 100),
  width = 1588)

# volvox-sorted.bam
reads <- jbrowse_alignments("https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam",
  locus,
  display = list(color = list(field = "mapq")))

fig <- jbrowse_stack(genes, reads)
print(fig)

Each reader returns the tables its track draws, and every band is an ordinary ggplot2 plot, so a figure is edited the usual way: draw one band alone with autoplot(reads, "pileup") and add a geom_*, a scale or a theme, or join your own table to genes$features. A feature track exports at the height the view gives it, so it drops the labels the view drops; change "fit" to "grow" to draw them all.

What it draws

Feature tracks (GFF3, GTF, BED, BigBed), variant tracks and multi-sample variant matrices (VCF), quantitative tracks (BigWig, multi-BigWig) and alignments tracks (BAM, CRAM). Several regions on screen draw end to end, as the view lays them out.

What it leaves out

A track ggjbrowse cannot read yet, such as an arc or GWAS track, and a setting it cannot draw, such as facets on a feature track, land in a comment block at the top of the script, which tells you where its figure differs from the view.

Where the data lives

The script opens each track by its path or URL, so every track needs one an R session can open.

  • A track opened with Choose File in jbrowse-web has neither, because the browser keeps the file handle to itself. The exporter leaves it out and names it in the header. JBrowse Desktop opens files by path, which the script uses directly.
  • A file over HTTP needs its index beside it at the usual name, or the track's declared index, which the script passes along.
  • A contig the assembly calls chr1 and the file calls 1 reads under the file's name, from the assembly's aliases.

Requirements

R with ggjbrowse: remotes::install_github("GMOD/ggjbrowse"). It brings ggplot2, patchwork and V8; no Bioconductor packages are needed. The script stops with the install line if the installed ggjbrowse is older than it needs.

How close to the view it is

The data, rows, colors and keys are the browser's own, computed by the same engine. The drawing is ggplot2's: its text, antialiasing and panel spacing, so the figure shows what the view shows without being a screenshot of it.