Create a new seq_track — seq

A track cell is partitioned into five nested zones:

Track outer margin — outermost band on the track cell; reserved for axis titles derived from the track mapping.
Track inner margin — separates titles from the window row.
Window outer margin — per-window spacer inside the track plot region.
Window inner margin — per-window band holding axis lines, ticks, and tick labels.
Plot area — where elements render.

Usage

seq_track(
  data = NULL,
  mapping = NULL,
  aesthetics = aes(),
  windows = NULL,
  track_id = NULL,
  direction = "right",
  track_width = 1,
  track_height = 1,
  scale_x = NULL,
  scale_y = NULL,
  scale_x2 = NULL,
  scale_y2 = NULL,
  y_windows = NULL,
  y_windows2 = NULL,
  track_outer_margin = 0.02,
  track_inner_margin = 0.02,
  window_outer_margin = 0,
  window_inner_margin = 0.02,
  window_margin = NULL,
  combine_windows = FALSE,
  combine_y_windows = FALSE,
  flip_x = FALSE,
  flip_y = FALSE,
  elements = list(),
  show_legend = TRUE,
  window_scale = NULL,
  ...
)

Arguments

data: A GRanges object providing the default data for elements in this track.
mapping: A SeqMap object from map() providing default aesthetic mappings.
aesthetics: A SeqAes object from aes() providing constant aesthetics.
windows: A GRanges object defining the genomic windows for this track. Elements cannot define their own windows — this is the only place windows are set.
track_id: Character. Unique identifier for this track, used for patchwork layout matching and cross-track link references.
direction: One of "right" (append to current row) or "under" (start new row). Ignored for the first track (always top-left) and when seq_plot() is given a layout string.
track_width: Relative width unit within its row. Default 1.
track_height: Relative height unit within its column. Default 1.
scale_x: Optional position scale for the primary x axis — a seq_scale_genomic() (default behaviour when NULL), seq_scale_continuous(limits = ...) for scalar data x, or seq_scale_discrete(levels = ...) for categorical x.
scale_y: Optional position scale for the primary y axis. Pass seq_scale_genomic(y_windows) to flip the track so genomic position runs along y; continuous / discrete scales are supported too.
scale_x2, scale_y2: Optional position scales for the secondary x and y axes. Elements routed to the secondary axis via map(axis.x = 2) or map(axis.y = 2) are positioned against these scales. When NULL, secondary scales are auto-inferred from the contributing elements at layoutGrid() time.
y_windows: Optional GRanges used as the genomic y-axis range when flipping the track. Setting this (or a SeqScaleGenomic scale_y) auto-enables uses_genomic_y.
y_windows2: Optional GRanges for a secondary genomic y axis.
track_outer_margin: Per-track outer margin in npc units. Scalar, length-4 c(bottom, left, top, right) (base-R par(mar = ...) order), or a named list with any of top, right, bottom, left. Default 0.02. Axis titles draw here.
track_inner_margin: Per-track inner margin. Same form as track_outer_margin. Default 0.02.
window_outer_margin: Per-window outer margin. Same form. Default 0. Optional spacer around each window.
window_inner_margin: Per-window inner margin. Same form. Default 0.02. Axis ticks and tick labels draw here.
window_margin: Deprecated. Use aes("window.gap.width" = <value>) on the plot or track aesthetics to control the inter-window gap. Passing a non-NULL value emits a deprecation warning and is otherwise ignored.
combine_windows: Logical. When TRUE, multi-region windows are concatenated into a single virtual panel — useful for drawing data that spans regions (e.g. inter-chromosomal Hi-C contacts) in one continuous track. Each original window's axis labels and title are still drawn, separated by a thin boundary marker. Default FALSE (multi-region windows render as separate panels).
combine_y_windows: Logical. Symmetric to combine_windows for the genomic y-axis (only relevant for tracks with multiple y_windows). Default FALSE.
flip_x, flip_y: Logical. When TRUE, mirror the x or y axis so low data values render at the high end of the panel and vice versa. Tick labels follow the same orientation.
elements: Optional list of SeqElement / SeqLink objects to pre-populate this track. Elements can also be added via addElement() or the %+% operator.
show_legend: Logical. When FALSE, this track contributes no legend keys regardless of element legend fields. Default TRUE.
window_scale: Numeric vector or NULL. Per-window x-axis scale factors (e.g. 1e-6 for Mb, 1e-3 for kb, 1 for bp). When NULL (default), the scale is inferred from the narrowest window. Length 1 applies the value to all windows; length equal to the number of windows uses values positionally; any other length triggers a warning and recycles with rep_len().
...: Additional arguments reserved for future use.

Value

A SeqTrackR6 instance (S3 class "SeqTrack").

Details

Axis lines sit at the boundary between the plot area and the window inner margin. Tick labels and axis titles pick up their text from the track's mapping: the x-axis title is the expression assigned to x, and the y-axis title is the expression assigned to y.

Examples

seq_track(track_id = "A")
#> <SeqTrack>
#>   Public:
#>     addElement: function (elem) 
#>     aesthetics: SeqAes
#>     clone: function (deep = FALSE) 
#>     collect_legend_keys: function () 
#>     combine_windows: FALSE
#>     combine_y_windows: FALSE
#>     data: NULL
#>     direction: right
#>     elements: list
#>     flip_x: FALSE
#>     flip_y: FALSE
#>     has_axis_x2: FALSE
#>     has_axis_y2: FALSE
#>     initialize: function (data = NULL, mapping = NULL, aesthetics = aes(), windows = NULL, 
#>     mapping: NULL
#>     resolved_theme: NULL
#>     scale_x: NULL
#>     scale_x2: NULL
#>     scale_y: NULL
#>     scale_y2: NULL
#>     show_legend: TRUE
#>     track_height: 1
#>     track_id: A
#>     track_inner_margin: list
#>     track_outer_margin: list
#>     track_width: 1
#>     uses_genomic_y: FALSE
#>     window_inner_margin: list
#>     window_margin: NULL
#>     window_outer_margin: list
#>     window_scale: NULL
#>     windows: NULL
#>     y_windows: NULL
#>     y_windows2: NULL