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

Project protein domains or genomic features through a spliced CDS map

On this page

• Usage
• Arguments
• Value
• Details
• See also
• Examples

Protein input uses one-based inclusive observed-residue coordinates. Genomic output preserves exon gaps in segments and uses the parent's biological strand; its outer envelope is not a claim that introns encode the domain. The inverse projects only intersections with coding bases, reports excluded bases, and uses the CDS feature ID as its protein coordinate namespace. This namespace is not an inferred protein accession. Inputs may supply a genomic segments list-column to describe disjoint genomic pieces.

Usage

Code

project_ggchord_features(
  feature_data,
  cds,
  from = c("protein", "genome"),
  codon_boundary = c("error", "expand")
)

Arguments

feature_data

Domain/feature data frame with feature_id, parent_id (or a single-valued parent_ids list-column), start and end.

cds

A map from build_ggchord_cds().

from

"protein" (default) or "genome".

codon_boundary

Inverse projection policy: "error" or "expand".

Value

Ordinary feature table with projected accver, start, end, strand, directionality, segments, parent IDs, genetic-code metadata, source coordinates and a ggchord_projection provenance attribute.

Details

Each domain retains its explicit feature_id, single CDS parent, source interval and source row. Source metadata survives with source_ prefixes on name conflicts. Multiple biological parents must be expanded explicitly before projection. Unknown parent, intronic-only, out-of-range, reversed, inconsistent-strand and ambiguous codon-boundary input produce errors. codon_boundary = "expand" explicitly permits an inverse interval to cover partial codons and reports this expansion; it does not modify source bases.

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)
# Select residues for display; this is not a detected domain.
selected <- tibble(
  feature_id = "selected_residues", parent_id = coding$feature_id,
  start = 2, end = 20
)
project_ggchord_features(selected, cds)