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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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Optimize sequence order and orientation for ribbon readability

On this page

• Usage
• Arguments
• Value
• See also
• Examples

Searches deterministic sequence-order and orientation changes that reduce weighted ribbon centre-line crossings and long chord spans. It never modifies the supplied data and never accepts a worse arrangement. Inputs above 2,000 ribbons use a deterministic 64-bin approximation and record approximate = TRUE in the returned report.

Usage

Code

optimize_ggchord_layout(
  seq_data,
  ribbon_data,
  seq_order = NULL,
  seq_orientation = NULL,
  optimize = c("order", "orientation"),
  weight = c("length", "count", "pident"),
  max_iter = 50L
)

Arguments

seq_data

Sequence data containing accver and length.

ribbon_data

Alignment data in ggchord ribbon format.

seq_order

Optional initial complete sequence order. The default uses the row order of seq_data.

seq_orientation

Optional initial orientation (1 or -1), scalar, complete vector, or named vector.

optimize

Any of "order" and "orientation".

weight

Objective weight: "length", "count", or "pident".

max_iter

Positive integer maximum number of improving search rounds.

Value

An object of class ggchord_layout_optimization containing seq_order, seq_orientation, before/after scores and a report.

See also

ggchord_data_contract

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send)
suggestion <- optimize_ggchord_layout(seqs, links, weight = "count")
suggestion$seq_order