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

Layered chord, circular and collinear sequence plots

On this page

• Usage
• Arguments
• Value
• See also
• Examples

Visualize multi-sequence alignments, a single circular sequence or linear collinearity using ggplot2's layered grammar. The constructor supplies data and validation. Add geometry with geom_*(), select a global view with coord_chord(), coord_circular() or coord_collinear(), and use mappings/scales for data-driven styles and themes for non-data appearance. The layout is computed lazily when the plot is built (e.g. via print(), ggsave(), or ggplot_build()).

Usage

Code

ggchord(
  seq_data,
  ribbon_data = NULL,
  gene_data = NULL,
  debug = FALSE,
  validate = c("warn", "error", "none"),
  ...
)

Arguments

seq_data

data.frame/tibble with accver and length, or a GRanges, Seqinfo or GInteractions object with known full sequence lengths, or a named nucleotide Biostrings XStringSet. Unnamed sequence objects must first use as_ggchord_seq() with explicit ids. Optional S4 inputs use as_ggchord_seq(). When present, sequence_unit must be "bp"; amino-acid intervals require an explicit CDS projection, and arbitrary character widths are not bp lengths.

ribbon_data

Optional alignment table with qaccver, saccver, qstart, qend, sstart and send. length and pident are optional unless requested by a mapping, filter or statistic. A GInteractions object uses as_ggchord_link() without inventing identity or alignment length.

gene_data

Optional table with accver, start, end and strand. Annotation (anno) may be omitted. Directional GRanges are accepted; use geom_feature(data = ...) for unknown-strand intervals.

debug

Logical. Whether to output debug information, default FALSE

validate

Character, default "warn". How to run the structured input-data validation (see validate_ggchord_data): "warn" emits a single summary warning when the data has problems and caches the full report on the plot object (p$ggchord$validation); "error" stops on severe problems; "none" skips the diagnostic validation (the cheap structural checks that prevent crashes are still performed).

...

Reserved for clear migration errors from removed constructor arguments. Use labs(), coord_chord() and theme() for presentation.

Value

A ggchord object (inherits from ggplot) to which geom_* layers can be added with +

See also

ggchord_api_contract, ggchord_data_contract, ggchord_layout_contract, view_ggchord()

Examples

Code

library(dplyr)
library(ggchord)
data(seq_data_example)
data(ribbon_data_example)
data(gene_data_example)

seqs <- seq_data_example |>
  select(accver, length)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send)
genes <- gene_data_example |>
  transmute(accver, start, end, strand = source_strand)
p <- ggchord(
  seq_data = seqs,
  ribbon_data = links,
  gene_data = genes
) +
  geom_seq() +
  geom_link_ribbon() +
  geom_gene()
print(p)