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

Guides for ggchord role aesthetics

On this page

• Usage
• Arguments
• Value

Thin wrappers around ggplot2::guide_legend() and ggplot2::guide_colourbar() with compact defaults suitable for chord diagrams. All ordinary ggplot2 guide arguments remain available.

Usage

Code

guide_ggchord_legend(
  title = ggplot2::waiver(),
  theme = NULL,
  position = NULL,
  direction = NULL,
  override.aes = list(),
  nrow = NULL,
  ncol = NULL,
  reverse = FALSE,
  order = 0,
  size_scale = 1,
  ...
)

guide_ggchord_colourbar(
  title = ggplot2::waiver(),
  theme = NULL,
  nbin = NULL,
  display = "raster",
  alpha = NA,
  draw.ulim = TRUE,
  draw.llim = TRUE,
  angle = NULL,
  position = NULL,
  direction = NULL,
  reverse = FALSE,
  order = 0,
  available_aes = c("colour", "color", "fill", "ribbon_fill", "gene_fill",
    "feature_fill", "region_fill"),
  size_scale = 1,
  ...
)

guide_ggchord_colorbar(
  title = ggplot2::waiver(),
  theme = NULL,
  nbin = NULL,
  display = "raster",
  alpha = NA,
  draw.ulim = TRUE,
  draw.llim = TRUE,
  angle = NULL,
  position = NULL,
  direction = NULL,
  reverse = FALSE,
  order = 0,
  available_aes = c("colour", "color", "fill", "ribbon_fill", "gene_fill",
    "feature_fill", "region_fill"),
  size_scale = 1,
  ...
)

Arguments

title

Guide title.

theme

Optional guide-specific theme.

position, direction

Guide position and direction.

override.aes

A list of legend-key aesthetic overrides.

nrow, ncol

Legend key layout.

reverse

Whether to reverse the key order.

order

Guide order.

size_scale

Positive multiplier for keys, spacing and typography. ggchord's automatically generated guides derive this from the active export device; direct calls default to 1.

...

Additional arguments passed to the corresponding ggplot2 guide.

nbin

Number of colourbar bins.

display

Colourbar display method.

alpha

Colourbar alpha override.

draw.ulim, draw.llim

Whether to draw upper/lower limit ticks.

angle

Tick-label angle.

available_aes

Aesthetics accepted by the guide.

Value

A ggplot2 guide object.