0.16.6 documentation

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

Development status and changes

On this page

• Current version
• RC fixes and progressive tutorials
• Changes in this version
• History and migration

Current version

These pages document ggchord 0.16.6, including cumulative changes from the 0.16.0–0.16.4 development phases. Consult GitHub Releases for formal tags, assets and publication dates.

RC fixes and progressive tutorials

• Progressive chord → collinear → plasmid modules, with schemas, import, layer construction and 13 source-backed plasmid cases.
• Refined four-sequence showcases, unified backgrounds and readable arrow legends; explicit guide text sizes are respected.
• Corrected inside primer placement and restriction registry side; tibble optional columns no longer cause spurious warnings.
• Retained candidate signatures, flexible forms, aliases and reexports; no new migration or deprecation. Dense labels can still be hidden or overlap across layers.

Changes in this version

• Reorganized learning, complete workflows, task guides and reference entry points. The first-plot lesson covers installation, minimal inputs, interpretation, saving and troubleshooting; task pages prepare their own objects.
• Complete Han function reference, including arguments, returns and explanatory prose, with same-page English switching and source-hash checks.
• Redesigned typography, chapter navigation, gallery and data encodings. Choose overall chord, single-sequence circular or local CDS views by question. Persistent navigation, mobile outlines and reserved image dimensions support long-page reading.
• Native pkgdown / Bootstrap 5 package-documentation layout with same-page language switching, search, contents, code disclosure and exact code copying.
• Chord, circular and collinear home-page examples; every documentation figure supports enlargement and actual-size viewing.
• Bundled or attributed real inputs, with explicit row/column selection before function calls.
• GC tracks computed from actual DNA and CDS membership checked by sequence identity.
• Standard 12-column BLAST workflows, real PAF/BLASTp input, CDS projection and format adaptation.
• Sequence/strand parameter formats, supported scope, recommendations and compatibility; native aa plotting remains a separate proposal.
• Fixes for empty primer layers and lost strand/user colours when gene tables omit optional annotation text.
• Full-resolution user artwork with lossless RGBA-preserving encoding. Candidate signatures and default palettes are unchanged; documentation palettes are explicit in code.

History and migration

The complete NEWS source retains past changes. Historical calls are not current examples; use the migration guide. Local development checks do not constitute formal release validation.