0.16.6 documentation

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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

Genomic sequence position scale

On this page

• Usage
• Arguments
• Value
• Examples

Controls major/minor genomic position breaks and labels independently for every sequence. The default domain is each sequence's [0, length] range; linear source-coordinate axes use the retained original genomic interval. This scale configures sequence axes in all three coordinate modes. To add an independent bp reference bar in a linear display, use geom_seq_scale().

Usage

Code

scale_seq_position_continuous(
  name = ggplot2::waiver(),
  breaks = ggplot2::waiver(),
  minor_breaks = ggplot2::waiver(),
  labels = ggplot2::waiver(),
  limits = NULL,
  expand = ggplot2::waiver(),
  oob = scales::censor,
  transform = "identity",
  n.breaks = 6,
  coordinates = c("relative", "source"),
  sequences = NULL,
  ...
)

Arguments

name

Scale name; position guides are disabled by default.

breaks, minor_breaks, labels, limits, expand, oob, transform, n.breaks

Standard continuous-scale controls.

coordinates

In linear layouts, use relative locus coordinates or original source coordinates retained by focus_ggchord_data(). This affects axis breaks and labels, not the underlying genomic geometry. Breaks returned in transformed scale space are converted back to genomic positions in every coordinate mode. Explicit breaks = NULL and minor_breaks = NULL suppress the corresponding ticks.

sequences

Optional character vector selecting sequence axes by their displayed accver. NULL keeps all axes; character() hides every axis. Focused or segmented views use window IDs, not parent source accessions. Unknown or undisplayed identifiers produce an error. This controls axis lines, ticks and labels together without dropping sequence geometry.

...

Additional arguments passed to ggplot2::continuous_scale().

Value

A ggplot2 continuous scale for the seq_position role.

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
ggchord(seq_data = seqs) +
  geom_seq() +
  coord_collinear() +
  scale_seq_position_continuous(breaks = seq(0, 100000, by = 20000))