plot.gTrack: plot

In mskilab/gTrack: Plotting multiple tracks of complex genomic data across multiple genomic windows

plot

Description

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

Usage

## S3 method for class '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(s)

Marcin Imielinski, Jeremiah Wala

mskilab/gTrack documentation built on Aug. 17, 2024, 6:10 a.m.