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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

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Focus ggchord data on one or more loci

On this page

• Usage
• Arguments
• Value
• See also

Crops sequence, gene and ribbon tables together and relocates retained coordinates to start at one in each output locus. Multiple loci from the same source sequence are supported; provide a unique locus_id column to control their output sequence IDs. Segmented annotations, cleavage positions and cached feature runs are cropped and relocated together. Source intervals, source origins and genomic left/right truncation flags are retained on the returned tables. Alignment cropping is a linear display projection, not a new alignment: identity is retained, and a scaled alignment length is marked as estimated.

Usage

Code

focus_ggchord_data(
  seq_data,
  ribbon_data = NULL,
  gene_data = NULL,
  loci,
  expand = 0,
  boundary = c("trim", "drop")
)

Arguments

seq_data

Sequence table containing accver and length.

ribbon_data

Optional ggchord alignment table.

gene_data

Optional gene or feature table.

loci

Data frame containing accver, start, and end, and optionally locus_id.

expand

Non-negative number of bases added on both sides, scalar or one value per locus.

boundary

Boundary policy. "trim" clips partially overlapping genes and alignments; "drop" keeps only rows fully contained in selected loci.

Value

A list of focused seq_data, ribbon_data, gene_data, normalized loci, and a compact report including retained/dropped source rows and truncated output rows. .source_origin is the original genomic position corresponding to local position one, including after repeated focusing.

See also

ggchord_data_contract