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

Get the chord layout from a ggchord plot

On this page

• Usage
• Arguments
• Value
• Examples

Returns the layout owned by an explicit ggchord plot. This avoids ambiguous cross-talk when several plots are built in one R session. For layer-aware tabular results, prefer export_ggchord_layout(). See ggchord_layout_contract for fields, units and cache ownership. Device/context changes invalidate cached estimates, including ordinary label layouts. build = FALSE then reports that no current layout is cached.

Usage

Code

get_chord_layout(plot, build = TRUE)

Arguments

plot

A ggchord plot.

build

Logical. Build the layout when it is not cached, default TRUE.

Value

A chord layout list containing the computed geometry (sequence arcs, ribbon polygons, gene arrows, axis elements, extremes, colors, etc.)

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
p <- ggchord(seq_data = seqs) +
  geom_seq()
get_chord_layout(p)$seqs