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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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Prepare independent windows for a segmented linear display

On this page

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

Crops through focus_ggchord_data() while retaining one sequence per window. Pass segments to coord_collinear() to place those sequences in shared display rows with explicit gaps and local reversals. Coordinates in the returned tables remain window-local and are never concatenated.

Usage

Code

segment_ggchord_data(
  seq_data,
  ribbon_data = NULL,
  gene_data = NULL,
  windows,
  point_data = NULL,
  cross_gap = c("split", "drop"),
  max_links = 10000
)

Arguments

seq_data

Full sequence table with unique accver and integer lengths.

ribbon_data

Optional paired interval table.

gene_data

Optional gene or generic feature table, including segments.

windows

Table with accver, start, end, unique locus_id, optional row_id (defaults to source accver) and orientation (1 or -1, defaults to 1). Bounds must be ordered, integral and within the sequence.

point_data

Optional point links with qaccver, saccver, qpos, spos.

cross_gap

How to handle interval links clipped by selected windows.

max_links

Positive integer upper bound on candidate ribbon/point copies. Increase explicitly for larger, intentionally overlapping views.

Value

A list containing focused seq_data, ribbon_data, gene_data, point_data, segments for the coordinate system, reversible source to window transforms, and a report with input row numbers for every output connection and omitted input rows. Each window retains its own source accession, origin, full length and truncation flags.

Details

cross_gap = "split" retains only the parts of each ribbon's linear endpoint correspondence that lie in both selected windows. Omitted regions are never bridged by one ribbon polygon. "drop" retains only links fully contained in a query and subject window. This is a display projection, not realignment. Point links survive only when both endpoints are retained. Overlapping windows can deliberately duplicate a source row; provenance identifies each copy, and max_links bounds the candidate expansion before allocation. Order in the window table is display order within each row.

See also

ggchord_data_contract

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
windows <- tibble(
  accver = rep(seqs$accver[1], 2),
  start = c(1, floor(seqs$length[1] * .65)),
  end = c(floor(seqs$length[1] * .4), seqs$length[1]),
  locus_id = c("left_window", "right_window"), row_id = seqs$accver[1]
)
segment_ggchord_data(slice_head(seqs, n = 1), windows = windows)