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

Draw primer binding ranges on a circular sequence

On this page

• Usage
• Arguments
• Value
• Examples

Primers are slender directional arcs drawn between the two lines of a double sequence backbone by default, not arrows in the feature stack. Add geom_primer_label_repel() for the matching unboxed label and leader.

Usage

Code

geom_primer(
  mapping = NULL,
  data = NULL,
  side = c("between", "outside", "inside"),
  arc_offset = 0.045,
  arc_linewidth = 0.026,
  colour = "#A020F0",
  position = NULL,
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping, data

Standard layer inputs.

side

Backbone lane used by the primer arc. "between" uses the backbone centre line; "outside" and "inside" use arc_offset.

arc_offset

Distance from the backbone centre when side is "outside" or "inside".

arc_linewidth

Radial width of the primer arc.

colour

Primer arc colour.

position, show.legend, inherit.aes

Standard layer arguments.

...

Additional parameters passed to geom_feature().

Value

A ggplot2 layer.

Examples

Code

library(dplyr)
data(plasmid_example_pUC19)
seqs <- plasmid_example_pUC19 |>
  select(accver, length)
primers <- find_primer_bindings(plasmid_example_pUC19, set = "universal")
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_primer(data = primers) +
  geom_primer_label_repel(data = primers) +
  coord_circular()