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

Chord diagram coordinate system

On this page

• Usage
• Arguments
• Value
• Examples

Controls global rotation, aspect ratio, coordinate limits, clipping and the strategy used to fit chord geometry and labels.

Usage

Code

coord_chord(
  rotation = 45,
  ratio = 1,
  xlim = NULL,
  ylim = NULL,
  expand = FALSE,
  clip = "off",
  fit = c("labels", "geometry", "manual")
)

Arguments

rotation

Global counterclockwise layout rotation in degrees, default 45, measured from the positive x axis. This rotates the complete layout; it does not change the biological strand or sequence orientation.

ratio

Fixed y/x aspect ratio, default 1.

xlim, ylim

Optional user limits. Explicit limits take priority over automatically fitted limits.

expand

Logical. Expand coordinate limits, default FALSE. Automatic fitting already includes a small safety margin; set TRUE to request the additional ggplot2 coordinate expansion.

clip

Whether drawing is clipped to the panel, default "off".

fit

Fitting strategy: "labels" includes measured label boxes, "geometry" fits geometric elements only, and "manual" requires explicit xlim and ylim.

Value

A Coord object for ggplot2 + composition

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
ggchord(seq_data = seqs) +
  geom_seq() +
  coord_chord(rotation = 20)