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

Highlight regions along sequence arcs

On this page

• Usage
• Arguments
• Value
• Examples

Draws rectangular bands on sequence arcs for one or more coordinate intervals. This is useful for marking loci, repeats, CRISPR arrays, or other user-defined regions without turning them into gene arrows.

Usage

Code

geom_seq_region(
  mapping = NULL,
  data = NULL,
  fill = "#F59E0B",
  colour = "#B45309",
  alpha = 0.25,
  region_width = 0.08,
  region_offset = 0,
  region_side = c("inside", "outside", "auto"),
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping

Default NULL (uses pre-computed data)

data

data.frame with at least accver, start, end; optional label, category and color. Factor start/end columns use their numeric labels, not level codes.

fill

Character. Default fill colour for regions, default "#F59E0B".

colour

Outline colour, default "#B45309".

alpha

Numeric (0-1). Region alpha, default 0.25.

region_width

Numeric. Band width in chord radius units, default 0.08.

region_offset

Numeric. Radial offset from the sequence arc, default 0.

region_side

Character. "inside", "outside" or "auto"; "auto" places regions inside the chord when possible.

position, show.legend, inherit.aes

Standard ggplot2 layer arguments.

...

Additional arguments passed to geom_polygon()

Value

A ggplot2 layer.

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send)
region <- tibble(
  accver = links$qaccver[1], start = min(links$qstart[1], links$qend[1]),
  end = max(links$qstart[1], links$qend[1])
)
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_seq_region(data = region)