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IGV-style nucleotide sequence track element

Source: R/seq_sequence.R
seq_sequence.Rd

Renders per-base coloured rectangles (and optionally letters) for genomic windows up to 200 bp wide. Wider windows emit a message and show nothing.

Usage

seq_sequence(
  data = NULL,
  mapping = NULL,
  aesthetics = aes(),
  genome = NULL,
  sequence = NULL,
  show_letters = FALSE,
  rect_height = NULL,
  colors = NULL,
  ...
)

Arguments

data

Ignored; sequence is fetched from genome or sequence.

mapping

Ignored.

aesthetics

Optional SeqAes. Supports color (letter color, defaults to matching the rectangle fill), background (letter background rectangle color, default NA).

genome

Character. BSgenome package name (e.g. "BSgenome.Hsapiens.UCSC.hg38"). Required when sequence is NULL.

sequence

Character string of nucleotides spanning the first window. When provided, genome is ignored.

show_letters

Logical. Show nucleotide letters when window width is <= 80 bp. Default FALSE.

rect_height

Numeric in (0, 1] or NULL. Fraction of track height used for the rectangles. Default NULL (full track height).

colors

Named character vector mapping nucleotide codes to hex colors. Defaults to UCSC standard: A="#00AA00", T="#FF0000", C="#0000FF", G="#FFB300".

...

Reserved.

Value

A SeqSequenceR6 instance.

Examples

# From BSgenome (requires BSgenome package)
if (FALSE) { # \dontrun{
  seq_sequence(genome = "BSgenome.Hsapiens.UCSC.hg38")
} # }

# From a string
seq_sequence(sequence = "ATCGATCGATCG", show_letters = TRUE)
#> <SeqSequence>
#>   Inherits from: <SeqElement>
#>   Public:
#>     .infer_scale_y: function () 
#>     aesthetics: SeqAes
#>     auto_legend: NULL
#>     clone: function (deep = FALSE) 
#>     collect_legend_keys: function () 
#>     colors: #00AA00 #FF0000 #0000FF #FFB300 #AAAAAA
#>     coordCanvas: NULL
#>     data: NULL
#>     draw: function () 
#>     genome: NULL
#>     initialize: function (data = NULL, mapping = NULL, aesthetics = aes(), genome = NULL, 
#>     legend: NULL
#>     mapping: NULL
#>     prep: function (layout_track, track_windows) 
#>     rect_height: NULL
#>     resolve: function (track_data = NULL, track_mapping = NULL) 
#>     resolved: NULL
#>     sequence: ATCGATCGATCG
#>     show_legend: TRUE
#>     show_letters: TRUE