0.16.6 documentation

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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

Draw restriction sites, labels and deterministic leaders

On this page

• Usage
• Arguments
• Value
• See also

Draw restriction sites, labels and deterministic leaders

Usage

Code

geom_restriction_site(
  mapping = NULL,
  data = NULL,
  label = TRUE,
  label_style = c("enzyme_position", "enzyme", "position"),
  label_order = c("auto", "enzyme_position", "position_enzyme"),
  label_side = c("outside", "inside", "auto"),
  leader = c("radial", "elbow", "straight"),
  min_label_gap = NULL,
  tick_length = 0.04,
  label_offset = 0.18,
  colour = "#202020",
  linewidth = 0.28,
  label_size = 3.2,
  fontface = NULL,
  family = NULL,
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping, data

Standard layer inputs.

label

Draw labels.

label_style

Label enzyme and position, enzyme only, or position only.

label_order

Automatic mirrored label order, enzyme first, or position first.

label_side

Draw labels outside, inside, or automatically.

leader

Leader routing style. The default "radial" measures actual text boxes, separates site anchors from final radial label positions, and routes either a direct connector or an independent radial stub plus fan segment. All enzyme-facing text edges follow one close circular contour in genomic order. Dense lateral clusters use evenly spaced contour fans, while sparse clusters retain their natural angular positions. The former "trunk" alias was removed in v0.16.1; use "radial". "straight" connects the tick tip directly to the final label edge, without detours around the sequence or other leaders. "elbow" uses one bend, starting with a local-normal departure where possible. Label positions and grouping are shared by all routing styles.

min_label_gap

Minimum genomic fraction between label slots. NULL derives a compact device-aware default from the rendered labels.

tick_length, label_offset

Local-normal distances.

colour, linewidth, label_size, fontface, family

Fixed appearance. With the default fontface = NULL, enzyme names are bold only when that enzyme cuts once in the supplied sequence; coordinates remain regular. An explicit fontface disables this automatic distinction.

position, show.legend, inherit.aes

Standard layer arguments.

...

Additional geom parameters.

Value

A ggplot2 layer.

See also

ggchord_data_contract