plot — plot.gTrack • gTrack

Plot gTrack object in multi-track genome browser view. gTracks will appear as stacked interval plots, line / bar / scatter plots, node-edge graphs, or triangle plots depending on the formatting settings and additional data (eg mdata) provided. gTracks can be drawn across several non-contiguous "windows" of the genome

Additional argument "links" takes a GRangesList of signed interval pairs (ie each item is length 2) representing genomic junctions as input. The junctions will be pointing right for + intervals and left for - intervals. The meta data of the links GRangesList ($lwd $col $lty) can be set to modulate the color, witwidth, and line style of the junction links .

usage: display(gt, win) # where win is a GRanges object display(gt) # this will show the entire span of seqinfo(gt) display(gt, '3:1e6-2e6') ## can use UCSC style strings display(gt, GRanges(20, IRanges(20e6, 21e6))) display(gt, '2', links = ra) # here, the entire chromosome 2 is shown, with rearrangements on top

# S3 method for gTrack
plot(
  x,
  y,
  windows = si2gr(seqinfo(x)),
  links = NULL,
  gap = NULL,
  y.heights = NULL,
  y.gaps = NULL,
  cex.xlabel = 1,
  cex.ylabel = 1,
  max.ranges = NA,
  links.feat = NULL,
  verbose = FALSE,
  legend.params = list(),
  ...
)

Arguments

windows: GRanges specifying windows to view (can also be GRangesList), default is whole genome
links: GRangesList of signed locus pairs specifying links to draw above the plot, optional GRangesList values meta data specify formatting of individual links: $label (text label), $col (line color), $lwd (line weight), $lty (line style), $arrow (arrow flag), $col.arrow (arrow color), $v (vertical spline bulge), $w (horizontal spline bulge)
gap: scalar numeric specifying gap between windows (only relevant if windows has length>1). Units of the gap are in genome coordinates
max.ranges: scalar numeric > 0 specifying max number of ranges to draw in a window (via sampling). If specified, overrides gTrack max.ranges formatting feature.
...,: additional last-minute formatting changes to the gtrack can be entered here (eg col = 'blue')

Author

Marcin Imielinski, Jeremiah Wala