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Genomic position scale

Source: R/scale.R
seq_scale_genomic.Rd

Creates a position scale based on genomic coordinates from a GRanges object. Used for axes that represent physical genome positions (bp, kb, Mb).

Usage

seq_scale_genomic(
  windows = NULL,
  scale_factor = NULL,
  breaks = NULL,
  minor_breaks = NULL,
  expand = c(0, 0),
  cap = c("capped", "full", "exact", "ticks"),
  labels = NULL,
  oob = c("exclude", "perimeter"),
  pretty = NULL
)

Arguments

windows

A GRanges object defining the genomic windows.

scale_factor

Numeric vector of per-window scale factors controlling the unit label (1e-6 = Mb, 1e-3 = kb, 1 = bp). If NULL, reads from mcols(windows)$scale or defaults to 1e-6.

breaks

Optional numeric vector of explicit break positions. When supplied, these are used instead of pretty()-generated breaks.

minor_breaks

Optional scalar (number of sub-divisions between major breaks) or numeric vector of explicit minor-break positions.

expand

Length-2 c(mul, add) specifying multiplicative and additive padding around the data range. Default c(0, 0) for genomic (windows already set the visible range).

cap

One of "capped" (axis line spans the break range), "full" (spans the expanded plot range), "exact" (spans the unexpanded data range), or "ticks" (no axis line, only ticks).

labels

Optional character vector of tick labels (same length as breaks). If NULL, breaks are formatted as decimal numbers.

oob

One of "exclude" (default — out-of-bounds data rows are dropped before the npc transform; a message() reports the count) or "perimeter" (clamped to the axis limits and counted).

pretty

Optional named list of arguments forwarded to base pretty() (e.g. list(min.n = 2, high.u.bias = 0)). Names that are not base pretty() arguments (such as bounds or f.min) will error from R.

Value

A SeqScaleGenomic / SeqPositionScale object.