0.16.6 documentation

Complete canonical API text; task articles explain the workflows. Tutorials

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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

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Convert genomic positions to or from a linear ggchord layout

On this page

• Usage
• Arguments
• Value
• Examples

Maps positions for ordinary ggplot2 annotation layers without modifying source tables. Inverse mapping returns the chosen relative or source bp. In a segmented layout, specify the window accession rather than its parent source accession. Positions outside that window, including display gaps, produce an error instead of being extrapolated into omitted sequence.

Usage

Code

map_ggchord_position(plot, accver, position, inverse = FALSE, source = FALSE)

Arguments

plot

A ggchord plot using coord_collinear().

accver

Sequence identifiers, scalar or one per position.

position

Numeric genomic positions, or layout x when inverse = TRUE.

inverse

Convert layout x back to bp.

source

Use original source coordinates after focusing.

Value

A data frame with accver, position, x and backbone y.

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
p <- ggchord(seq_data = seqs) +
  geom_seq() +
  coord_collinear()
map_ggchord_position(p, seqs$accver[1], position = 100)