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

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Add a sequence label layer

On this page

• Usage
• Arguments
• Value
• Examples

Places sequence labels at the midpoint of each sequence arc, radially offset from the arc. Labels can be styled via their radial offset, rotation, font size, text orientation and justification.

Usage

Code

geom_seq_label(
  mapping = NULL,
  data = NULL,
  seq_label_radius = 1,
  seq_label_rotation = NULL,
  labels = NULL,
  seq_label_orientation = c("arc", "horizontal"),
  seq_label_hjust = NULL,
  seq_label_vjust = NULL,
  check_overlap = FALSE,
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping

Default NULL (uses pre-computed data)

data

Default NULL (retrieved automatically from the layout)

seq_label_radius

Optional numeric/vector. Radial position of the labels as a multiplier of the sequence arc radius: 1 is on the arc, > 1 places the label outside (away from the chord center) and < 1 places it inside, default 1 Explicit values are incompatible with coord_collinear(), which places sequence labels beside the left endpoint of each horizontal track.

seq_label_rotation

Optional numeric/vector. Additional label rotation (degrees) on top of the arc-aligned orientation, default NULL (0). Ignored when seq_label_orientation = "horizontal".

labels

Optional character vector. Override the label texts (defaults to the sequence labels from geom_seq() or the sequence IDs)

seq_label_orientation

Character, default "arc". Label text orientation: "arc" rotates the text along the sequence arc (and keeps it readable), "horizontal" draws every label horizontally, extending away from the chord center.

seq_label_hjust

Optional numeric/vector. Horizontal justification of the labels, default NULL. The default arc orientation uses -0.2 so the text sits just inside the sequence; with seq_label_orientation = "horizontal" the justification is chosen automatically so the text extends away from the chord center.

seq_label_vjust

Optional numeric/vector. Vertical justification of the labels, default NULL (0.5).

check_overlap

Logical, default FALSE. When TRUE, labels that would overlap a previously drawn label are skipped (ggplot2's geom_text() option).

position, show.legend, inherit.aes

Standard ggplot2 layer arguments.

...

Additional arguments passed to geom_text()

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() +
  geom_seq_label()