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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

Project explicitly ungapped protein links to genomic coding segments

On this page

• Usage
• Arguments
• Value
• See also
• Examples

Splits paired protein intervals wherever either CDS crosses a segment boundary, retaining query/subject roles and genomic endpoint directions. This is a codon-coordinate correspondence, not a new nucleotide alignment. Source protein identity and length remain prefixed metadata and are never emitted as nucleotide pident or alignment length. General gapped alignments require explicit per-column alignment information and cannot be projected by this endpoint-only helper.

Usage

Code

project_ggchord_links(link_data, cds, ungapped = FALSE)

Arguments

link_data

Data frame with qfeature_id, sfeature_id identifying CDS models and ordered inclusive protein qstart, qend, sstart, send. Query and subject residue spans must be equal. If present, gapopen must be zero and source length must equal this residue span.

cds

A map from build_ggchord_cds().

ungapped

Must explicitly be TRUE, confirming an ungapped residue correspondence rather than inferring it from equal endpoint spans.

Value

A paired genomic interval table with CDS parent IDs, source row, piece number, genomic strands, projected_bases, source-prefixed input metadata and projection provenance. No alignment identity is computed.

See also

ggchord_data_contract

Examples

Code

library(dplyr)
data(plasmid_example_pUC19)
feature_source <- find_common_features(plasmid_example_pUC19)
features <- feature_source |>
  select(accver, start, end, strand, type, anno)
coding <- features |>
  filter(anno == "AmpR", type == "CDS") |>
  select(accver, start, end, strand) |>
  mutate(feature_id = paste(accver, "AmpR", sep = ":"), phase = 0)
cds <- build_ggchord_cds(coding, genetic_code = 11)
# Self-correspondence of one real CDS, solely to demonstrate coordinate conversion.
# The same observed residues are paired, so the correspondence is ungapped.
selected <- tibble(
  qfeature_id = coding$feature_id, sfeature_id = coding$feature_id,
  qstart = 1, qend = 20, sstart = 1, send = 20
)
project_ggchord_links(selected, cds, ungapped = TRUE)