0.16.6 documentation

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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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Mark cropped ends of linear sequences

On this page

• Usage
• Arguments
• Value
• Examples

Adds two short diagonal strokes at each truncated sequence end in coord_collinear(). Metadata returned by focus_ggchord_data() determines the truncated genomic ends; reversed sequence orientation moves each mark to the corresponding displayed end. These marks are decorations and do not change the source sequence or feature coordinates.

Usage

Code

geom_seq_break(
  mapping = NULL,
  data = NULL,
  break_width = 0.02,
  break_height = 0.04,
  linewidth = 0.4,
  colour = "#3D4348",
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping, data

Standard layer mapping and sequence data. By default, use the plot's sequence table. Truncation is read from .truncated_left/.truncated_right, with source interval and length metadata as fallback when available.

break_width, break_height

Width and height of the complete break mark in linear layout units. These are layout distances, not millimetres.

linewidth, colour

Fixed line appearance. Ordinary visual aesthetics can also be mapped and controlled by their ggplot2 scales.

position, show.legend, inherit.aes

Standard ggplot2 layer arguments.

...

Additional parameters passed to ggplot2::geom_path().

Value

A ggplot2 layer. Other ggchord coordinate systems are unsupported.

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
loci <- tibble(
  accver = seqs$accver, start = floor(seqs$length * .25),
  end = floor(seqs$length * .75)
)
focused <- focus_ggchord_data(seqs, loci = loci)
ggchord(seq_data = focused$seq_data) +
  geom_seq() +
  geom_seq_break() +
  coord_collinear()