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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

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Deduplicate alignment ribbons

On this page

• Usage
• Arguments
• Value
• See also
• Examples

Removes fully duplicated, coordinate-near-duplicated or highly overlapping alignment blocks within each (query, subject) pair and keeps the best representative per keep.

Usage

Code

deduplicate_ggchord_ribbons(
  ribbon_data,
  tolerance = 0,
  by = c("exact", "coordinates", "overlap"),
  keep = c("best_pident", "longest", "first"),
  min_reciprocal_overlap = 0.9
)

Arguments

ribbon_data

data.frame in ribbon_data format.

tolerance

Numeric, default 0. Maximum absolute difference (in bp) allowed on each of qstart/qend/sstart/send for two rows to count as coordinate duplicates (used with by = "coordinates").

by

Character, default "exact". "exact" removes rows with identical pair and coordinates; "coordinates" additionally treats rows within tolerance bp as duplicates; "overlap" treats blocks whose reciprocal overlap is at least min_reciprocal_overlap on both sequences as duplicates. Each interval must meet the threshold, not only the shorter one. Opposite relative endpoint directions are kept as distinct relationships by all methods. Single-base endpoints use supplied strand/direction evidence; otherwise their direction is unknown.

keep

Character, default "best_pident". Which representative to keep: "best_pident" (highest pident), "longest" (longest length) or "first" (first occurrence in the input).

min_reciprocal_overlap

Numeric (0-1), default 0.9. Reciprocal overlap threshold used with by = "overlap".

Value

A list with data (deduplicated data frame with source_rows attribute) and report (n_input/n_kept/n_removed plus a data.frame of removed rows with row, duplicate_of and reason).

See also

ggchord_data_contract

Examples

Code

library(dplyr)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send, pident, length)
out <- deduplicate_ggchord_ribbons(links, by = "overlap")
out$report