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

Place a quantitative layer in an explicit sequence-local band

On this page

• Usage
• Arguments
• Value
• Examples

Layers with the same track ID share a band and numerical scale across all displayed sequences and windows. Their declarations must agree. Outside means positive local normal (up in linear coordinates), inside negative. The coordinate system resolves physical placement; feature-stack lanes and sequence ring radii are unrelated to track IDs.

Usage

Code

position_track(
  track,
  side = c("outside", "inside"),
  order = 1,
  width = grid::unit(4, "mm"),
  gap = grid::unit(1, "mm")
)

Arguments

track

One stable nonempty character ID.

side

"outside" or "inside".

order

Finite ordering priority, nearest band first. Ties use ID order.

width, gap

Positive band width and nonnegative preceding gap. Absolute grid units (mm, cm, inches or points) are resolved against the render context. Numeric values retain native layout units. Numeric per-sequence vectors/lists follow the usual sequence parameter formats.

Value

A ggplot2 Position object for the three track geoms.

Examples

Code

position_track("depth", width = unit(4, "mm"))