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

Frequently asked questions

On this page

• Why are labels different after resizing?
• Why did an old parameter stop working?
• Why is a feature rejected as a gene?
• Why is a ribbon missing in linear mode?
• Can the package compute alignments or validate primer experiments?
• Is a measured diagnostic a release certification?
• Where should I report a problem?

Why are labels different after resizing?

The available physical space changed. Use explicit-size preview and saving. Check hidden-label diagnostics; do not infer missing input rows from absent text.

Why did an old parameter stop working?

The API cleanup removed execution of old aliases. Use the migration table. Do not mix old and new spellings for one semantic setting. The colour/color function spelling aliases remain, with colour preferred in documentation.

Why is a feature rejected as a gene?

The gene shortcut requires known +/- strand. Keep unknown strand in a general feature layer; do not guess +. Amino-acid intervals require explicit projection.

Why is a ribbon missing in linear mode?

By default ribbons connect adjacent displayed sequences. Inspect pair selection, clipping and validation. Use explicit pairs or adjacent_only = FALSE deliberately. This default does not remove original input records.

Can the package compute alignments or validate primer experiments?

It visualizes supplied alignments and computational search results. It does not run BLAST, infer clusters from names or validate wet-lab outcomes. Search confidence is not a probability. See recognition limitations.

Is a measured diagnostic a release certification?

No. It describes a requested render. Platform/device/font checks, full vignettes and package checks belong to an explicitly authorized release. See the release acceptance record for the actual scope of verification.

Where should I report a problem?

Use the issue tracker with a small input, package/ggplot2 versions, code, intended width/height, device and diagnostic output. Avoid attaching private sequence data; a synthetic reproduction is usually enough.