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Complete canonical API text; task articles explain the workflows. Tutorials

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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

Convert paired genomic intervals to ggchord links

On this page

• Usage
• Arguments
• Value
• See also
• Examples

For GInteractions, the first stored anchor becomes query and the second becomes subject. Their order is never sorted or swapped by this adapter. A source object that already canonicalized its anchors cannot recover their earlier biological host/virus roles; establish those roles before conversion. Negative-strand anchor endpoints run from end to start. Unknown-strand anchors retain increasing coordinates, their * strand and orientation_known = FALSE; increasing order is not direction evidence. Interval interactions do not imply a pairwise alignment: identity and alignment length are not inferred from anchor widths.

Usage

Code

as_ggchord_link(x, mapping = NULL)

Arguments

x

A data frame or GInteractions object.

mapping

Optional named character vector mapping canonical link roles to source columns, as in as_ggchord_seq().

Value

An ordinary data frame with qaccver, saccver, qstart, qend, sstart, send and source metadata. Paired objects also retain anchor indices, source row/name, anchor strands, anchor metadata prefixed with query_/subject_, and object-level metadata in the conversion attribute.

See also

ggchord_data_contract

Examples

Code

library(dplyr)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send)
as_ggchord_link(links)