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

Validate explicit genome and contig relationships

On this page

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

Checks relational keys without deriving genome membership, changing sequence order or joining contigs into a continuous sequence. Original input tables and their metadata are returned unchanged. Sequence lengths and annotation coordinates can be checked separately with validate_ggchord_data().

Usage

Code

validate_ggchord_hierarchy(seq_data, genomes, strict = FALSE)

Arguments

seq_data

A data frame containing accver and genome foreign keys.

genomes

A data frame containing a unique genome primary key.

strict

Logical. Stop if relational errors are present; warnings about genomes without contigs do not cause failure.

Value

A list with valid, unchanged seq_data and genomes, an issues data frame (table, row, column, category, severity, message), and contigs, a genome-order table with genome, n_contigs, and sequence_rows/accvers list-columns for each valid unique genome key.

Details

A sequence belongs to exactly one genome. Sequence accver values must be globally unique, including when local contig names would be reused by two genomes. Supply distinct explicit identifiers before validation; this function never prefixes or rewrites them. Genome rows with no contigs are reported as warnings, and remain in the returned genome table.

See also

ggchord_data_contract

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
contigs <- seqs |>
  mutate(genome = accver)
genomes <- tibble(genome = seqs$accver)
validate_ggchord_hierarchy(contigs, genomes)