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

3.1 DNA, annotations and 13 references

On this page

• Tables and optional information
• Inspect bundled real records
• Import your own plasmid
• A progressive case sequence

A single-sequence circular map starts with two columns. Feature, primer and restriction searches additionally need real DNA; existing annotations can be drawn directly without running recognition again.

Tables and optional information

Input	Required content	Optional content
Backbone	accver, length; exactly one sequence	label for display; sequence for searches
Features	accver, start, end and declared directionality	type, anno/label, feature_id and shape categories
Primers	Computed binding interval, strand/name roles required by the geom	Recognition and provenance fields
Restriction sites	Position/name roles required by the geom	Enzyme catalogue, methylation assumption and filter provenance

Backbones do not require DNA. Prefer search-result tables for the latter layers and consult their help for detailed fields. Unknown-strand annotations belong in generic feature layers.

Inspect bundled real records

Code

library(ggchord)
library(dplyr)
plasmid_example_pUC19 |> select(accver, length)
find_common_features(plasmid_example_pUC19) |> select(accver, start, end, strand, type, anno) |> slice_head(n = 5)

The compact names retain ggchord’s early BLAST workflow history. accver need not be a database accession. Full DNA and length must agree. Recognition is computational matching, not experimental validation.

Import your own plasmid

read_fasta_lengths() reads IDs and full lengths only. Searches additionally need actual DNA, for example read with optional Biostrings readDNAStringSet() and as.character(), retaining matching IDs. GFF3/BED/GenBank or GRanges annotations follow the format guide, retaining provenance. Handle circular-origin and segmented records according to the reader contract; do not invent one continuous interval by merging every segment.

A progressive case sequence

3.2 builds pUC19 layer by layer; 3.3 explains recognition, primers and restriction sites; 3.4 uses all 13 unique repository plasmids; 3.5 completes the dense pETDuet-1 map. pUC19c is a compatibility alias, not a 14th case.