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

2.1 Reuse chord input tables

On this page

• The same three tables
• Obtain the inputs
• Current conversion boundaries

Collinearity extends ggchord’s original chord grammar into a linear view. The design goal is to retain shared data and layers, switching coordinates wherever the contracts permit.

The same three tables

Input	Required columns	Linear interpretation
seq_data	accver, length	One sequence per row with a shared bp x scale
ribbon_data	qaccver, saccver, qstart, qend, sstart, send	An observed interval correspondence between rows
gene_data	accver, start, end, strand	Genes separated above/below rows by a Position

Optional fields and the historical BLAST naming follow 1.1. Identity needs pident; labels need anno. Source fields preserve coordinates in local windows; display gaps do not represent invented DNA lengths.

Obtain the inputs

Reuse the FASTA/GFF3/BLAST workflow in 1.2, or import PAF, GRanges and GInteractions through adapters. Protein alignments require explicit CDS projection; aa endpoints must not be presented as bp.

Current conversion boundaries

The next page demonstrates replacing coord alone. Explicit circular radius, curvature, ring and radial sequence-label placement are rejected by the current linear contract rather than silently ignored. Keep coordinate-specific styling in the appropriate showcase. Perfect conversion of every possible composition remains a design goal, not a current guarantee.

Linear views default to adjacent displayed rows. Set adjacent_only = FALSE in shared layers to retain the chord link set. Choose manual sequence directions or coordinate-owned automatic orientation, not both at once.