0.16.6 documentation

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

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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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Compute local ribbon density as a ggchord stat

On this page

• Usage
• Arguments
• Value
• See also

Keeps one output ribbon per input row while measuring density in normalized query/subject midpoint bins. The computed variables are the same as stat_ribbon_bundle(), so density can be mapped with aes(ribbon_alpha = after_stat(density)).

Usage

Code

stat_ribbon_density(
  mapping = NULL,
  data = NULL,
  bins = 80L,
  weight = c("length", "count", "pident"),
  group_by = NULL,
  position = "identity",
  show.legend = TRUE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping, data

Standard layer mapping and data arguments.

bins

Positive integer number of normalized midpoint bins per sequence.

weight

Density weight: "length", "count", or "pident".

group_by

Optional columns that define independent density groups.

position, show.legend, inherit.aes

Standard ggplot2 layer arguments.

...

Ribbon geometry and appearance arguments passed to geom_link_ribbon().

Value

A ggchord ribbon layer.

See also

ggchord_data_contract