0.16.6 documentation

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

Site guide · find your task

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

Arrange primer labels and leaders

On this page

• Usage
• Arguments
• Value

Primer labels are unboxed, use the primer colour, and show one-based inclusive binding coordinates by default. Their leaders start at the directional primer arc's arrow tip (the primer 3-prime end). Factor start/end columns use their numeric labels for both displayed text and retained binding-coordinate metadata, matching feature geometry.

Usage

Code

geom_primer_label_repel(
  mapping = NULL,
  data = NULL,
  side = c("outside", "inside"),
  show_location = TRUE,
  colour = "#A020F0",
  max_overlaps = Inf,
  position = NULL,
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping, data

Standard layer inputs.

side

Side of the backbone on which the primer callout is arranged. "inside" retains the inner label layout, including when exterior restriction or feature labels share the map. The default is "outside".

show_location

Include the binding range in the label.

colour

Primer arc colour.

max_overlaps

Maximum unresolved overlaps.

position, show.legend, inherit.aes

Standard layer arguments.

...

Additional parameters passed to geom_feature().

Value

A composite text and leader-line layer.