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

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Add a sequence arc layer

On this page

• Usage
• Arguments
• Value
• Examples

Draws arcs (or straight lines, depending on the curvature setting) representing sequences in the chord diagram. Sequence layout parameters (order, orientation, radius, curvature, colors, etc.) are specified here.

Usage

Code

geom_seq(
  mapping = NULL,
  data = NULL,
  seq_order = NULL,
  seq_orientation = NULL,
  seq_gap = NULL,
  seq_radius = NULL,
  seq_curvature = NULL,
  seq_style = c("auto", "single", "double", "band"),
  seq_backbone_gap = 0.025,
  seq_backbone_width = 0.035,
  linewidth = 0.9,
  position = "identity",
  show.legend = TRUE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping

Default NULL (uses pre-computed data)

data

Default NULL (retrieved automatically from the layout)

seq_order

Optional character vector. Specifies the drawing order of sequences

seq_orientation

Optional numeric (1 or -1). Sequence orientation, default 1

seq_gap

Optional numeric. Gap proportion between sequences, default 0.03 in chord coordinates. In coord_collinear(), a positive distance between consecutive backbones as a proportion of the longest backbone's width, default 0.3. The final sequence's gap is unused in linear layouts. Segmented linear displays measure it against the longest display row; windows in one row must request the same gap, and only gaps between rows affect vertical placement.

seq_radius

Optional numeric (> 0). Sequence arc radius, default 1.0

seq_curvature

Optional numeric. Signed arc bow (0=straight, 1=standard arc, negative=opposite bow), default 1.0. Finite positive and negative values are accepted without clipping; magnitudes above 1 amplify the bow.

seq_style

Backbone geometry. "auto" uses a double backbone in coord_circular() and the historical single backbone in coord_chord().

seq_backbone_gap

Gap between double backbone lines.

seq_backbone_width

Width of a band backbone.

linewidth

Arc line width, default 0.9

position, show.legend, inherit.aes

Standard ggplot2 layer arguments.

...

Additional fixed path aesthetics. colour (or color) sets seq_colour. Explicit fixed values take precedence over matching mappings; omit fixed arguments to retain mapped styles.

Value

A ggplot2 layer.

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
ggchord(seq_data = seqs) +
  geom_seq()