0.16.6 documentation

Complete canonical API text; task articles explain the workflows. Tutorials

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Setup and learning paths

HomeInstall and prepare the environmentChoose your learning module

Module I · Chord

1.1 Tables and field meanings1.2 Produce and import comparisons1.3 Build the layers step by step1.4 Direction, curvature and clearance1.5 Filter and summarize links1.6 Full source-file workflow1.7 Complete chord showcase

Module II · Collinear

2.1 Reuse chord input tables2.2 Switch coordinates and add layers2.3 Routes, clearance and the ruler2.4 Compare CDS neighbourhoods2.5 Focus, anchors and segments2.6 Complete collinear showcase

Module III · Plasmid

3.1 DNA, annotations and 13 references3.2 From a circle to annotation layers3.3 Features, primers and restriction3.4 Thirteen plasmid references3.5 Complete plasmid cases

Consult as needed · Data and layers

Prepare tables and coordinatesImport and convert dataImport nucleotide and protein alignmentsProject protein intervals to genomic coordinatesFeatures, stacking and genomic decorationLabels and local placementQuantitative tracksMappings, scales, guides and themesSet values by sequence and strandCommon adjustments and grammarExport, preview and diagnostics

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Set a named track's numerical height scale

On this page

• Usage
• Arguments
• Value
• Examples

Uses an independent continuous scale for each track ID. The same ID shares its domain across sequences, windows and layers. The scale controls height, not colour. A numerical axis is drawn by default; guide = "none" hides it.

Usage

Code

scale_track_value_continuous(
  track,
  name = track,
  limits = NULL,
  breaks = ggplot2::waiver(),
  labels = ggplot2::waiver(),
  transform = "identity",
  oob = scales::censor,
  unit = NULL,
  guide = c("axis", "none"),
  ...
)

Arguments

track

Track ID from position_track().

name

Axis title, default the track ID.

limits, breaks, labels, transform, oob

Standard continuous-scale controls.

unit

Optional data-unit label retained in track exports.

guide

"axis" or "none" for the numerical track axis.

...

Additional ggplot2 continuous-scale arguments.

Value

A ggplot2 scale, scoped to this track.

Examples

Code

scale_track_value_continuous("coverage", limits = c(0, 100), unit = "reads")