Skip to contents

Strand-classified SV reconstruction arches

Source: R/seq_recon.R
seq_recon.Rd

Inherits everything from seq_arch() and additionally classifies each link by strand orientation and chromosome pair, drawing each class on a fixed tier with a class-specific color. Use to summarise structural variant calls.

Usage

seq_recon(
  data = NULL,
  mapping = NULL,
  t0 = NULL,
  t1 = NULL,
  aesthetics = aes(),
  drawClasses = c("Inversion", "Dup/Del", "Translocation"),
  ...
)

Arguments

data

Optional GRanges or data.frame. Falls back to the parent track's data.

mapping

Optional map().

t0, t1

Track identifiers. Locked to the parent track when added inside a seq_track().

aesthetics

Optional aes(): color, linewidth, orientation ("+" / "-" / "*"), curve ("length", "equal", or numeric).

drawClasses

Character vector of tier labels to render (default: c("Inversion", "Dup/Del", "Translocation")).

...

Reserved.

Value

A SeqReconR6 instance.

Details

Default colors come from flexoki_palette() and can be overridden via aes(h2hColor=, t2tColor=, dupColor=, delColor=, transColor=).

Both strand0 and strand1 must be specified in map() — seq_recon errors at prep() time if either is absent.