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

Draw point-to-point sequence links

On this page

• Usage
• Arguments
• Value
• Examples

Requires qaccver, saccver, qpos and spos. Positions use the same genomic coordinates as sequence tracks. Curves run from query to subject; an arrow supplied by arrow() therefore points to the subject by default.

Usage

Code

geom_link_line(
  mapping = NULL,
  data = NULL,
  link_type = c("curve", "straight"),
  link_gap = NULL,
  link_ctrl_point = NULL,
  link_avoid = c("none", "smooth", "uniform"),
  link_branch = c("none", "query", "subject"),
  link_branch_fraction = 0.15,
  arrow = NULL,
  colour = "#59636D",
  alpha = 0.6,
  linewidth = 0.4,
  linetype = 1,
  position = "identity",
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping, data

Standard ggplot2 mapping and layer data, including data functions.

link_type

Either "curve" (default) or "straight".

link_gap

Explicit endpoint spacing. With the default link_avoid = "none", NULL uses a fixed spacing of 0.035. Set link_avoid to "smooth" or "uniform" to opt in to entity-aware endpoint spacing.

link_ctrl_point

Bezier control points: two numbers, four numbers, or a list per input row.

link_avoid

One of "none" (default), "smooth", or "uniform". Explicit gap takes precedence.

link_branch

Share equal query or subject endpoints: "none", "query", "subject".

link_branch_fraction

Shared length relative to the shortest member, in (0, 0.5].

arrow

A grid arrow specification, or NULL.

colour, alpha, linewidth, linetype

Fixed styles; mappings use link_* aesthetics. An explicitly supplied fixed value takes precedence over the matching mapping. Omit the fixed argument to retain a mapped style, including an inherited mapping when inherit.aes = TRUE.

position, show.legend, inherit.aes

Standard ggplot2 layer arguments.

...

Additional path parameters.

Value

A ggplot2 layer.

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send, pident, length)
points <- links |>
  transmute(qaccver, saccver,
    qpos = floor((qstart + qend) / 2),
    spos = floor((sstart + send) / 2)
  )
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_link_line(data = points)