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

Feature shape scale

On this page

• Usage
• Arguments
• Value

Maps feature categories to the geometry types understood by geom_feature(), including full/compact/promoter/primer arrows, markers, blocks, capped lines, chevrons, and lollipops. capped_line is an unfilled interval with short terminal caps. Shape values affect the actual feature geometry as well as its legend key.

Usage

Code

scale_feature_shape_manual(
  ...,
  values,
  name = "Feature",
  limits = NULL,
  guide = "none"
)

Arguments

...

Arguments passed to ggplot2::discrete_scale().

values

A named or unnamed character vector of feature geometry names.

name

Scale and guide title, default "Feature".

limits

Optional category order. Named values use their name order by default so shape and fill guides can merge cleanly.

guide

Guide specification. The default is "none" because geom_feature() combines shape silhouettes into its fill legend when both aesthetics describe the same feature categories. Supply guide_ggchord_legend() for a separate shape guide.

Value

A ggplot2 discrete scale for the feature_shape aesthetic.