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

Example gene annotation data

On this page

• Usage
• Format

A compact plotting fixture generated deterministically from examples/gene_track.tsv. Eight features of varied visible lengths are distributed across each sequence and favour informative annotations. Because the source records are strongly strand-biased, the demonstration strand alternates between "+" and "-"; the biological source value remains available as source_strand.

Usage

Code

gene_data_example

Format

A data frame containing the following columns:

• accver: Sequence accession/version or an unchanged custom identifier

• start: Gene start position

• end: Gene end position

• strand: Strand direction (+/-)

• anno: Gene annotation category

• source_strand: Strand direction in the source annotation file