Chromosome ideogram from cytogenetic bands

Draws a chromosome ideogram: each cytoband becomes a filled rectangle shaded by its Giemsa stain (gpos25 darkens through gpos100; gneg is white; stalk and gvar carry their conventional colors). Paired acen bands within a window render as two inward-pointing red triangles, marking the centromere.

Usage

seq_ideogram(
  data = NULL,
  mapping = NULL,
  aesthetics = aes(),
  scope = "window",
  style = "block",
  highlight_range = NULL,
  ...
)

Arguments

data

Optional GRanges of cytobands. Falls back to the parent track's data. Must carry a gieStain mcol unless a stain mapping is supplied.

mapping

Optional map(). Recognised: stain.

aesthetics

Optional aes(): color (band border color, default "black"), linewidth (band border width, default 0.1), outline (nested aes() controlling the chromosome's outer perimeter outline: sub-keys col, lwd, visible), highlight (nested aes() controlling the scope = "full" highlight rectangle: sub-keys fill, col, lwd, alpha), telomere.radius (numeric; corner radius as a fraction of band height for style = "rounded"; 1.0 = full half-circle cap).

scope

Character. One of "window" (default — only bands overlapping the track windows are drawn) or "full" (the whole chromosome is drawn rescaled to fill the panel; the current window region is overlaid as a translucent highlight rectangle).

style

Character. One of "block" (default — rectangular bands) or "rounded" (rounded telomere caps on the leftmost and rightmost bands).

highlight_range

Optional GRanges. Only honoured when scope = "full". When set, the highlight rectangle marks this range instead of the parent track's windows. Lets you set the track's windows to span the full chromosome (so the x-axis reads chromosome coordinates) while still highlighting a sub-range.

...

Reserved.

Value

A SeqIdeogramR6 instance.

Details

The simplest call supplies a GRanges of cytobands — use load_cytobands() to load the bundled hg38 table:

cb <- load_cytobands()
seq_plot() %|%
  seq_track(track_id = "Ideo",
            windows = default_genome_windows()) %+%
  seq_ideogram(data = cb)

Map a non-standard stain column with map(stain = my_col).