Package 'ggchord'

Description

Uses ggplot2's standard composition semantics for layers, scales, themes, coordinates and annotations.

Usage

## S3 method for class 'ggchord'
e1 + e2

Arguments

Value

A ggchord object

Description

GRanges coordinates are already one-based inclusive and are not shifted. Strand * is retained as source_strand, while the output uses strand = "." and directionality = "none". Use the returned table in geom_feature(data = ...) to preserve nondirectional intervals; geom_gene() requires directional gene input. No unknown strand is invented as +.

Usage

as_ggchord_feature(x, mapping = NULL)

Arguments

Value

An ordinary feature data frame with accver, start, end, strand, directionality, retained metadata and conversion provenance. Conflicting metadata names receive a metadata_ prefix; the attribute's column_map records the output name.

See Also

ggchord_data_contract

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(gene_data_example)
genes <- gene_data_example |>
  transmute(accver, start, end, strand = source_strand)
renamed <- genes |>
  rename(chrom = accver, left = start, right = end)
features <- as_ggchord_feature(renamed,
  mapping = c(accver = "chrom", start = "left", end = "right")
)
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_feature(data = features)

Description

For GInteractions, the first stored anchor becomes query and the second becomes subject. Their order is never sorted or swapped by this adapter. A source object that already canonicalized its anchors cannot recover their earlier biological host/virus roles; establish those roles before conversion. Negative-strand anchor endpoints run from end to start. Unknown-strand anchors retain increasing coordinates, their * strand and orientation_known = FALSE; increasing order is not direction evidence. Interval interactions do not imply a pairwise alignment: identity and alignment length are not inferred from anchor widths.

Usage

as_ggchord_link(x, mapping = NULL)

Arguments

Value

An ordinary data frame with qaccver, saccver, qstart, qend, sstart, send and source metadata. Paired objects also retain anchor indices, source row/name, anchor strands, anchor metadata prefixed with query_/subject_, and object-level metadata in the conversion attribute.

See Also

ggchord_data_contract

Examples

library(dplyr)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send)
as_ggchord_link(links)

Description

Explicit adapters return ordinary data frames. Optional interval packages are loaded only when their objects are supplied; drawing never installs or runs external data preparation. Supported S4 inputs supplied directly to ggchord or its layers use the same adapters. Identifiers are kept verbatim.

Usage

as_ggchord_seq(x, mapping = NULL, lengths = NULL, ids = NULL)

Arguments

Details

For a GRanges object, lengths come from its Seqinfo, never from the maximum observed feature endpoint. A GInteractions object uses the same information from its common regions. Only sequence names used by the supplied intervals are returned; a Seqinfo object returns all its entries. Unknown lengths require explicit lengths or corrected source information.

XStringSet and XString inputs use their stored sequence widths. Set names are identifiers; unnamed sequences require explicit ids. Explicit IDs must agree with existing nonempty names, so identifiers and accession versions are never silently rewritten. sequence_unit records "bp", "aa", or "character"; amino-acid widths are not nucleotide coordinates. These non-nucleotide tables remain available for data workflows, but ggchord() rejects them as genomic sequence input. Project amino-acid intervals with build_ggchord_cds() and project_ggchord_features() or project_ggchord_links() before using known nucleotide sequence lengths. Empty sequences are rejected like other zero lengths.

Value

An ordinary data frame with accver, length and retained metadata. Its ggchord_conversion attribute records input class, coordinate system, column renaming, object-level metadata, and upstream import/conversion provenance when present. No genomic coordinates or accession versions are guessed or rewritten.

See Also

ggchord_data_contract

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
renamed <- seqs |>
  rename(chrom = accver, size = length)
as_ggchord_seq(renamed, mapping = c(accver = "chrom", length = "size"))

Description

Combines the errors and warnings tables into a single data.frame and adds a severity column, which is convenient for filtering, exporting or printing the full report programmatically.

Usage

## S3 method for class 'ggchord_validation'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Arguments

Value

A data.frame with columns table, category, row, column, message and severity.

See Also

ggchord_data_contract

Description

Builds a mapping from observed protein residues to genomic coding bases. CDS rows sharing feature_id form one coding model. Their genomic intervals must be non-overlapping and have one sequence and known strand. Segments are ordered in transcription direction, increasing on + and decreasing on -. An explicit segment_order overrides genomic sorting, allowing a declared circular-origin join. A segments list-column can declare segment_order for transcription order, including reverse-strand and origin joins; otherwise its pieces follow genomic strand order. Generic segment_index identifiers are preserved as source metadata and do not define transcription order. Nested phases may be supplied or derived from an explicit first phase or codon_start - 1; no phase is guessed from the genomic envelope. Trans-spliced models spanning different sequence IDs are rejected.

Usage

build_ggchord_cds(cds_data, genetic_code = NULL, partial = c("error", "trim"))

Arguments

Details

GFF3 phase counts bases from a segment's biological 5-prime end to the next codon boundary. Only the first phase is skipped; later phases validate the accumulated coding length, retaining bases of codons split across exons. partial = "error" rejects partial ends. Explicit "trim" permits a nonzero first phase, partial-end flags and incomplete terminal codons, and excludes bases without complete codons. Residue one then means the first complete observed codon, not an inferred position in an unobserved protein.

Optional partial5, partial3, genetic_code, and protein_id columns must agree within each model. A nonzero initial phase requires partial5; if absent it is recorded as partial5. A terminal remainder similarly records partial3 unless a conflicting explicit flag is supplied. Genetic-code IDs are retained as metadata: coordinate projection does not translate sequence, identify stop codons, or infer a genetic code. codon_count includes any source terminal stop codon. Frameshifts, ribosomal slippage and translation exceptions or non-join location operators cannot be represented by a simple triplet map and are rejected when declared. No full protein length or identity is inferred.

Value

A ggchord_cds list containing a models summary, transcription- ordered segments per feature, original source_data and provenance. Segment cds_start/cds_end identify complete-codon nucleotide positions; genomic coordinates and original row numbers remain available.

See Also

https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md

ggchord_data_contract

Examples

library(dplyr)
data(plasmid_example_pUC19)
feature_source <- find_common_features(plasmid_example_pUC19)
features <- feature_source |>
  select(accver, start, end, strand, type, anno)
coding <- features |>
  filter(anno == "AmpR", type == "CDS") |>
  select(accver, start, end, strand) |>
  mutate(feature_id = paste(accver, "AmpR", sep = ":"), phase = 0)
cds <- build_ggchord_cds(coding, genetic_code = 11)
cds$features

Description

Aggregates nearby alignment ribbons on a normalized query/subject grid. Bundling is always explicit: geom_link_ribbon() continues to draw one ribbon per input row unless the returned data are supplied by the user. Groups use relative endpoint direction, so reversing both ends can remain in the same group. The envelope follows the first row's absolute directions; length and identity are length-weighted source means (length is rounded), not statistics of a newly computed alignment. Conflicting extra metadata become typed missing values. Use group_by to keep source categories separate and retain the original input with the source-row report. Single-base endpoint rows stay independent because their endpoint order cannot define an absolute aggregate direction. Density can still count them without merging their geometry.

Usage

bundle_ggchord_ribbons(
  ribbon_data,
  seq_data,
  bins = 80L,
  min_bundle = 2L,
  weight = c("length", "count", "pident"),
  group_by = NULL
)

Arguments

Value

A list with data and report. The data include .bundle_n, .bundle_weight, and .bundle_density; the report maps each output row back to its source rows.

See Also

ggchord_data_contract

Examples

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)
out <- bundle_ggchord_ribbons(links, seqs, bins = 30)
out$report

Description

Applies a conservative, predictable set of cleaning policies to the three ggchord tables and returns the cleaned copies plus a full report. The original data frames are never modified. Nothing is dropped silently: every change (including every dropped row) is recorded in report with the original row number, the reason, the original value(s) and the new value(s). Its historical sorting default differs deliberately from preparation's direction-preserving default. Use reversed_interval = "keep" for directional links and circular-origin features; sorting endpoints loses information that a later workflow cannot reconstruct.

Usage

clean_ggchord_data(
  seq_data,
  ribbon_data = NULL,
  gene_data = NULL,
  unknown_id = c("drop", "error", "keep"),
  out_of_range = c("clip", "drop", "error", "keep"),
  reversed_interval = c("sort", "drop", "error", "keep"),
  invalid_pident = c("clip", "drop", "error", "keep"),
  empty_annotation = c("keep", "drop", "replace"),
  replacement_annotation = "unannotated"
)

Arguments

Value

A list with four components: seq_data, ribbon_data, gene_data (cleaned copies) and report (a data.frame with columns table, row (original row number), column, reason, original_value, new_value and action).

See Also

ggchord_data_contract

Examples

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)
# Deliberate diagnostic error in a copy; source observations remain unchanged.
problem <- links |>
  slice_head(n = 2) |>
  mutate(qaccver = replace(qaccver, 2, "absent"))
cleaned <- clean_ggchord_data(seqs, problem, unknown_id = "drop")
cleaned$report

Description

Controls global rotation, aspect ratio, coordinate limits, clipping and the strategy used to fit chord geometry and labels.

Usage

coord_chord(
  rotation = 45,
  ratio = 1,
  xlim = NULL,
  ylim = NULL,
  expand = FALSE,
  clip = "off",
  fit = c("labels", "geometry", "manual")
)

Arguments

Value

A Coord object for ggplot2 + composition

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
ggchord(seq_data = seqs) +
  geom_seq() +
  coord_chord(rotation = 20)

Description

Single-sequence circular coordinate system

Usage

coord_circular(
  rotation = 0,
  direction = c("clockwise", "counterclockwise"),
  gap = 0,
  ratio = 1,
  xlim = NULL,
  ylim = NULL,
  expand = FALSE,
  clip = "off",
  fit = c("labels", "geometry", "manual")
)

Arguments

Value

A Coord object for ggplot2 composition.

Description

Draws sequences as left-aligned horizontal backbones, ordered from top to bottom by geom_seq(seq_order = ...). All sequences share one linear bp scale. seq_orientation = -1 reverses a sequence together with its features, links and axis without modifying the input data.

Usage

coord_collinear(
  ratio = 1,
  xlim = NULL,
  ylim = NULL,
  expand = FALSE,
  clip = "off",
  fit = c("labels", "geometry", "manual"),
  align = c("left", "center", "right"),
  anchor = NULL,
  orientation = c("manual", "auto"),
  min_support = 0.1,
  segments = NULL,
  segment_gap = 100
)

Arguments

Details

In this coordinate system, geom_seq(seq_gap = ...) specifies the distance between consecutive backbones as a proportion of the longest backbone's width (default 0.3). Positive Position offsets point upward and negative offsets downward, independently of sequence orientation. Sequence labels appear to the left of their backbone. Automatic feature labels use local horizontal rows; fixed radial labels are vertical and tangent labels are horizontal. Label side "outside" means above and "inside" below.

Explicit sequence radius, curvature, ring mappings/scales and sequence-label radius cannot be converted and produce an error. Remove these arguments when switching from coord_chord(). Circular-only primer, restriction-site and centre-label layers require coord_circular(); use geom_feature() for general linear annotations. Cross-track links may cross intervening tracks. Explicit link control points use the exported linear layout x/y units; the longest backbone has width 2 (the longest complete display row when segments is supplied). The circular external = FALSE feature-label constraint cannot be converted; remove it to use linear label rows. Gene/feature repel layout modes share the linear row strategy rather than selecting circular label tracks.

align and anchor control a reversible display translation. With no anchor, the selected edge or centre of each complete sequence is placed at x = 0. With an anchor, the selected edge or centre of each anchor interval is placed at x = 0 instead. Left and right refer to the displayed interval, after orientation has been applied. Genomic input coordinates stay unchanged. Sequence order is never changed by alignment or automatic orientation.

orientation = "auto" evaluates interval links against earlier displayed sequences and chooses the direction supported by the larger aligned-interval weight. The first sequence fixes the reference direction. Ambiguous, insufficiently supported and unconnected sequences retain their initial direction, with evidence recorded in the exported layout diagnostics. This is a display heuristic, not a biological strand assignment or a guarantee of a global optimum. It cannot be combined with an explicit geom_seq(seq_orientation = ...).

With segments, each accession remains an independent window but windows sharing row_id occupy one display row. Their table order is left to right; align applies to the whole row. segment_gap reserves display space in bp scale units, independently of omitted genomic length. Internal ends receive break marks. Use segment_ggchord_data() to crop/split input first. Local reversal comes from the table's orientation, so automatic orientation, explicit sequence orientation and anchor conflict with this mode. Ribbon adjacency follows display rows; same-row ribbons are omitted with a report, and explicit same-row pairs or point links are unsupported.

Value

A ggplot2 Coord object for composition with a ggchord plot.

Examples

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)
ggchord(seq_data = seqs, ribbon_data = links) +
  geom_seq() +
  geom_link_ribbon() +
  geom_seq_label() +
  coord_collinear(orientation = "auto")

Description

Removes fully duplicated, coordinate-near-duplicated or highly overlapping alignment blocks within each (query, subject) pair and keeps the best representative per keep.

Usage

deduplicate_ggchord_ribbons(
  ribbon_data,
  tolerance = 0,
  by = c("exact", "coordinates", "overlap"),
  keep = c("best_pident", "longest", "first"),
  min_reciprocal_overlap = 0.9
)

Arguments

Value

A list with data (deduplicated data frame with source_rows attribute) and report (n_input/n_kept/n_removed plus a data.frame of removed rows with row, duplicate_of and reason).

See Also

ggchord_data_contract

Examples

library(dplyr)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send, pident, length)
out <- deduplicate_ggchord_ribbons(links, by = "overlap")
out$report

Description

Builds on a temporary device of the requested kind and measures the actual single panel after gtable layout, then refines physical geometry within a bounded render-local context. The original plot and its layout cache are left unchanged. Standard saving continues to use ggplot2::ggsave().

Usage

diagnose_ggchord(
  plot,
  width = 7,
  height = 5,
  units = c("in", "cm", "mm", "px"),
  device = c("png", "pdf", "svg"),
  dpi = 144,
  min_size = 2,
  min_linewidth = 0.2,
  colour_vision = FALSE
)

Arguments

Details

Results describe evidence, not a general quality certificate. Checks cover registered vertex bounds, measured text, small text/lines, oversized guides, and existing label/track diagnostics. Objects outside a panel with clip = "off" are legal when they still fit the canvas. Unregistered custom grobs, arrowhead extents, font embedding/fallback and cross-application transparency are not certified. Device warnings remain in the report.

Grayscale suggestions compare luminance of opaque discrete mapped colours (difference below 0.05); continuous gradients are deliberately excluded. With colour_vision = TRUE, optional colorspace public simulations for protan/deutan/tritan at severity 1 in linear RGB flag Lab distances below 10. These heuristic thresholds ignore spatial context, alpha compositing and viewing conditions, and never automatically change the plot or fail a run.

Value

A ggchord_diagnostics list with measurement, checks, text and guide measurements, colour suggestions, existing label_diagnostics, annotation_registry, track_registry, track_diagnostics, and captured device warnings. Field units and provenance are described in ggchord_layout_contract. measurement$status concerns panel measurement only; it never means that all quality or portability checks passed.

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
p <- ggchord(seq_data = seqs) +
  geom_seq()
diagnose_ggchord(p, width = 8, height = 6, units = "in", device = "png")

Description

Builds a ggchord plot and returns selected computed geometry in a stable, layer-aware structure. Every exported row records its source layer and, where applicable, its source input row. Original mapped columns already attached to the geometry are preserved. This is the recommended interface for consuming layout tables; get_chord_layout() remains available for the complete layout list. Both retain their documented fields. See ggchord_layout_contract for units, provenance and stability boundaries.

Usage

export_ggchord_layout(
  plot,
  include = c("seq", "ribbon", "gene", "feature", "labels", "axis", "track"),
  original_data = FALSE
)

Arguments

Value

An object of class ggchord_layout_export. Selected component names contain data frames. Circular layouts additionally contain an annotation_registry data frame. Its inner rows expose the physical track, radial width and boundaries; outer rows expose region, sector, annotation class, dominant and actual band, spill reason, leader-crossing count, slot, bounding box and leader corridor. Explicitly inside primer and restriction callouts register measured inner boxes rather than exterior bands or slots. The metadata member records rotation, aspect ratio, limits, coordinate units and transformation state. Collinear layouts instead include sequence_layout, containing each sequence's horizontal range, backbone y, orientation, units per bp, reversible x offset, anchor and source origin. orientation_diagnostics records directional support, confidence and unresolved cases. Position lanes remain local offsets and are not circular physical tracks. Their label_diagnostics records placed or hidden labels after shared linear collision handling, including source layer, row, reason and leader collisions. connection_report records retained and omitted ribbon input rows with a selection reason. When converted inputs are present, conversion_reports retains their conversion attributes, including source class, column renaming, sequence information and object metadata. Sequence break marks are included under seq. Segmented linear displays retain one sequence_layout row per window, including row_id, segment order, break flags and display gap_bp. Source accession, origin/end/full length, local orientation, x offset and units per bp describe each reversible piece; gaps have no source mapping. Automatic segment break paths have .decoration = "segment_break" in the sequence geometry. gap_bp is display spacing, not omitted length. Quantitative geometry is selected with track; track_registry records each ID/sequence band, source layers, numerical limits, unit and physical measurement status. track_diagnostics records retained/missing/clipped source rows. Numerical track axes and explicit bp reference bars are included under axis; axis_selection records selected sequence axes. Explicit label shrinking adds label_fit_diagnostics, preserving original text, requested/minimum/final sizes and fallback or hiding reasons. render_context distinguishes layout-only estimates from actual panel measurements. For a target-size measured report use diagnose_ggchord().

Examples

library(dplyr)
library(ggchord)
data(seq_data_example)
data(ribbon_data_example)
p <- ggchord(seq_data_example, ribbon_data_example) +
  geom_seq() +
  geom_link_ribbon()
exported <- export_ggchord_layout(p, include = c("seq", "ribbon"))
names(exported)

Description

Keeps the ribbon rows that satisfy all requested criteria and optionally sorts them. The returned data frame keeps every extra column and the original column order; the original row numbers are attached as the source_rows attribute. Each non-NULL numeric threshold must be one finite number. Columns used by a numeric criterion must be numeric; missing values fail that criterion.

Usage

filter_ggchord_ribbons(
  ribbon_data,
  seq_ids = NULL,
  min_pident = NULL,
  max_pident = NULL,
  min_length = NULL,
  max_evalue = NULL,
  min_bitscore = NULL,
  min_query_coverage = NULL,
  min_subject_coverage = NULL,
  keep_pairs = NULL,
  drop_self_links = TRUE,
  sort_by = NULL
)

Arguments

Value

A list with data (the filtered data frame, with source_rows attribute) and report (n_input/n_kept/n_removed, removed_by_reason, removed_rows and kept_rows).

See Also

ggchord_data_contract

Examples

library(dplyr)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send, pident, length)
out <- filter_ggchord_ribbons(links, min_pident = 95, min_length = 500)
out$report

Description

Filter restriction sites for display

Usage

filter_restriction_sites(
  sites,
  set = c("all", "unique", "unique_dual", "six_plus", "unique_6plus", "commercial",
    "reference"),
  enzymes = NULL,
  min_site_length = NULL,
  cuts = NULL,
  window = NULL,
  commercial_only = FALSE,
  parent_set = c("all", "commercial_all", "commercial_nonredundant")
)

Arguments

Value

A row subset whose biological coordinates are unchanged.

See Also

ggchord_data_contract

Examples

data(plasmid_example_pUC19)
sites <- find_restriction_sites(plasmid_example_pUC19,
  enzymes = c("EcoRI", "BamHI", "HindIII"))
unique_sites <- filter_restriction_sites(sites, set = "unique")

Description

Searches the built-in common-feature database (or a compatible custom database) using curated exact-sequence annotations, exact DNA, and the detection mode stored for each database record. Restriction sites are intentionally outside this API; use find_restriction_sites() for those. Protein matching uses a standard-code six-frame translation, without alternative initiation, splicing or origin-crossing protein matches. Source geneticCode metadata does not select a translation table. For nonstandard codes use mode = "dna" or external code-aware analysis. confidence is a deterministic heuristic label, not a probability or experimental confirmation. identity and coverage describe the reported match method, not independently validated biological function.

Usage

find_common_features(
  sequence,
  database = NULL,
  types = NULL,
  features = NULL,
  circular = TRUE,
  mode = c("auto", "dna", "protein"),
  min_protein_identity = 0.9,
  min_protein_coverage = 0.8,
  resolve = c("best", "all")
)

Arguments

Value

A data frame directly usable by geom_feature() and geom_feature_label_repel(). feature_class and feature_shape provide semantic metadata and a geometry hint; neither affects radial stacking. Explicit user aesthetics and scales still take priority. Its segments list-column preserves the biological feature's segment structure.

See Also

ggchord_data_contract

Description

Selects targets by feature_id and expands their genomic bounds using biological upstream/downstream directions. For a negative-strand target, upstream extends towards larger genomic coordinates. Unknown or bidirectional strands require equal upstream and downstream distances. Windows are clipped to the known full sequence length; clipping is reported.

Usage

find_ggchord_loci(
  seq_data,
  feature_data,
  targets,
  upstream = 0,
  downstream = 0
)

Arguments

Details

Repeated rows with the same feature_id represent segments of one target and must belong to the same sequence and strand. Their outer bounds define the target window. Different targets always produce separate windows, including overlapping targets on the same sequence. No intervening sequence is removed, concatenated or locally reversed. Ordered one-based inclusive genomic coordinates are required; origin-spanning circular features and protein coordinates need an explicit conversion before this operation.

The returned locus_id equals target_id. Pass the returned table as loci to focus_ggchord_data() to create independent focused sequences named by those IDs, including multiple windows from one source sequence.

Value

An ordinary data frame in target order with target_id, locus_id, accver, start, end, strand, unexpanded target_start and target_end, requested extensions, and clipped_left/clipped_right. The target_source_rows list column identifies feature input rows used for each target. Coordinates refer to the supplied sequence table; no implicit change from focused coordinates to an earlier source is made.

See Also

ggchord_data_contract

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(gene_data_example)
genes <- gene_data_example |>
  transmute(accver, start, end, strand = source_strand)
genes <- genes |>
  mutate(feature_id = paste(accver, start, end, sep = ":"))
find_ggchord_loci(seqs, genes, targets = genes$feature_id[1], upstream = 100, downstream = 100)

Description

Searches each distinct oligonucleotide once on both target strands and then attaches all catalogue aliases. Exact matching is the default. Optional three_prime matching uses the longest exact 3-prime suffix available, with no mismatches, and is intended for inspecting partial annealing rather than silently treating it as a full match. Binding hits are sequence-search results, not experimental validation. melting_temperature uses the Wallace composition estimate unless source annotations supply it; ambiguous bases do not contribute to that estimate.

Usage

find_primer_bindings(
  sequence,
  primers = NULL,
  set = c("universal", "all", "reference"),
  match = c("exact", "three_prime"),
  min_annealed_bases = 15L,
  circular = TRUE,
  unique_only = FALSE
)

Arguments

Value

One row per binding site. The aliases list-column preserves every catalogue name associated with the matched oligonucleotide.

See Also

ggchord_data_contract

Examples

target <- c(circle = "TTGCAAAAACG")
find_primer_bindings(
  target, primers = c(test = "ACGTTGCA"),
  min_annealed_bases = 8
)

Description

Find restriction pattern matches and cleavage coordinates

Usage

find_restriction_sites(
  sequence,
  enzymes = NULL,
  patterns = NULL,
  circular = TRUE,
  database = NULL,
  methylation = c("auto", "none", "dam_dcm")
)

Arguments

Value

One row per pattern match without display filtering or deduplication. Methylation-aware columns include methylation_status, blocked_by, display_warning, methylation_motif, and sensitivity_source. enzyme_site_count records the number of distinct cleavage/display positions for that enzyme on the complete supplied sequence, so it remains stable after display filtering. For an exactly recognized bundled reference sequence, the reference_enzyme_profiles attribute records its saved display set for use by filter_restriction_sites().

See Also

ggchord_data_contract

Description

Crops sequence, gene and ribbon tables together and relocates retained coordinates to start at one in each output locus. Multiple loci from the same source sequence are supported; provide a unique locus_id column to control their output sequence IDs. Segmented annotations, cleavage positions and cached feature runs are cropped and relocated together. Source intervals, source origins and genomic left/right truncation flags are retained on the returned tables. Alignment cropping is a linear display projection, not a new alignment: identity is retained, and a scaled alignment length is marked as estimated.

Usage

focus_ggchord_data(
  seq_data,
  ribbon_data = NULL,
  gene_data = NULL,
  loci,
  expand = 0,
  boundary = c("trim", "drop")
)

Arguments

Value

A list of focused seq_data, ribbon_data, gene_data, normalized loci, and a compact report including retained/dropped source rows and truncated output rows. .source_origin is the original genomic position corresponding to local position one, including after repeated focusing.

See Also

ggchord_data_contract

Description

Applies the same explicit loci and output IDs as focus_ggchord_data() and segment_ggchord_data(). It never averages, interpolates, rescales values, or creates boundary samples. Missing values remain missing. Subsequent track layers group by the returned window accession, so separate windows cannot be joined by a line. Source coordinates and original row lineage survive repeated focusing.

Usage

focus_ggchord_track(
  data,
  seq_data,
  loci,
  type = c("point", "interval"),
  boundary = c("trim", "drop")
)

Arguments

Value

An ordinary data frame with focused coordinates. Its ggchord_track_focus attribute reports output-to-input rows and omitted input rows; ⁠.source_*⁠ columns retain earliest source coordinates.

See Also

ggchord_data_contract

Examples

library(ggchord)
library(dplyr)
data(plasmid_example_pUC19)
track_seq <- plasmid_example_pUC19 |>
  select(accver, length)
starts <- seq.int(1L, track_seq$length, by = 100L)
gc_fraction <- function(sequence) {
  bases <- strsplit(sequence, "")[[1]]
  mean(bases %in% c("G", "C"))
}
bins <- tibble(
  accver = track_seq$accver,
  start = starts,
  end = pmin(starts + 99L, track_seq$length)
) |>
  rowwise() |>
  mutate(gc = gc_fraction(substr(plasmid_example_pUC19$sequence, start, end))) |>
  ungroup()
loci <- tibble(accver = track_seq$accver, start = 501, end = 2000)
focus_ggchord_track(bins, track_seq, loci, type = "interval")

Description

A compact plotting fixture generated deterministically from examples/gene_track.tsv. Eight features of varied visible lengths are distributed across each sequence and favour informative annotations. Because the source records are strongly strand-biased, the demonstration strand alternates between "+" and "-"; the biological source value remains available as source_strand.

Usage

gene_data_example

Format

A data frame containing the following columns:

• accver: Sequence accession/version or an unchanged custom identifier

• start: Gene start position

• end: Gene end position

• strand: Strand direction (+/-)

• anno: Gene annotation category

• source_strand: Strand direction in the source annotation file

Description

A general layer for CDS, tRNA, rRNA, repeat, CRISPR, promoter or user-defined features. It supports directional arrows, blocks, notched chevrons and lollipops, all generated against the sequence's real local curve. Feature fill and geometry use independent role-specific scales.

Usage

geom_feature(
  mapping = NULL,
  data = NULL,
  shape = "arrow",
  width = NULL,
  arrow_head_length = 0.04,
  arrow_head_width = 1,
  arrow_head_style = c("shouldered", "flush", "triangle"),
  short_feature = c("auto", "wedge", "block"),
  segment_boundaries = TRUE,
  boundary_colour = "#666666",
  boundary_linewidth = 0.25,
  boundary_linetype = "22",
  position = "identity",
  show.legend = TRUE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A ggplot2 layer.

Examples

library(dplyr)
data(plasmid_example_pUC19)
seqs <- plasmid_example_pUC19 |>
  select(accver, length)
feature_source <- find_common_features(plasmid_example_pUC19)
features <- feature_source |>
  select(accver, start, end, strand, type, anno)
# ASCII display copy for the default PDF help-example device.
features <- features |>
  mutate(anno = gsub("\u03b1", "alpha", anno, fixed = TRUE))
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_feature(
    data = features,
    shape = "block"
  ) +
  coord_circular()

Description

Label generic genomic features

Usage

geom_feature_label(
  mapping = NULL,
  data = NULL,
  label_orientation = c("feature", "horizontal", "radial", "tangent"),
  label_side = c("outside", "inside", "auto"),
  label_overlap = c("hide", "nudge", "allow"),
  label_wrap = NULL,
  label_rotation = NULL,
  label_radial_offset = 0.04,
  label_circum_offset = NULL,
  label_circum_limit = NULL,
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A ggplot2 layer.

Description

Automatically arrange generic feature labels

Usage

geom_feature_label_repel(
  mapping = NULL,
  data = NULL,
  label_layout = c("feature", "radial", "auto", "callout"),
  label_wrap = NULL,
  label_fit = c("wrap", "none", "ellipsis", "auto", "shrink"),
  label_max_lines = 2L,
  label_side = c("outside", "inside", "auto"),
  max_overlaps = Inf,
  external = TRUE,
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  label_min_size = 1.5,
  label_segment_overlap = "fade",
  label_segment_overlap_alpha = 0.18,
  label_segment_linetype = "auto",
  ...
)

Arguments

Details

Manual label rotation, offsets, orientation and overlap policy belong to geom_feature_label(). Their ⁠label_*⁠ controls are rejected by automatic layers rather than silently ignored.

Value

A composite text and leader-line layer.

Examples

library(dplyr)
data(plasmid_example_pUC19)
seqs <- plasmid_example_pUC19 |>
  select(accver, length)
feature_source <- find_common_features(plasmid_example_pUC19)
features <- feature_source |>
  slice_head(n = 4) |>
  select(accver, start, end, strand, type, anno)
# ASCII display copy for the default PDF help-example device.
features <- features |>
  mutate(anno = gsub("\u03b1", "alpha", anno, fixed = TRUE))
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_feature(data = features, position = position_plasmid()) +
  geom_feature_label_repel(data = features, position = position_plasmid()) +
  coord_circular()

Description

A concise plasmid-map preset built on geom_feature(). It uses the same generic feature engine, while selecting a compact circular track, protruding shouldered block arrows, and dashed internal segment joins.

Usage

geom_feature_plasmid(
  mapping = NULL,
  data = NULL,
  shape = "arrow",
  width = 0.058,
  arrow_head_length = 0.068,
  arrow_head_width = 1.42,
  arrow_head_style = "shouldered",
  short_feature = "auto",
  segment_boundaries = TRUE,
  boundary_colour = "#666666",
  boundary_linewidth = 0.25,
  boundary_linetype = "22",
  position = NULL,
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A ggplot2 layer.

Description

A directed-gene shortcut using the generic geom_feature() constructor with arrow geometry and the independent gene_fill role. Gene input still requires a known + or - strand; use geom_feature() for unknown strands. The gene fill scale is kept independent from the ribbon's fill scale via a separate internal aesthetic used by the ribbon layer.

Usage

geom_gene(
  mapping = NULL,
  data = NULL,
  width = NULL,
  arrow_head_length = 0.04,
  arrow_head_width = 1,
  arrow_head_style = c("shouldered", "flush", "triangle"),
  short_feature = c("auto", "wedge", "block"),
  position = "identity",
  show.legend = TRUE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A ggplot2 layer. To annotate the genes with their labels, add a geom_gene_label() layer.

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(gene_data_example)
genes <- gene_data_example |>
  transmute(accver, start, end, strand = source_strand)
ggchord(seq_data = seqs, gene_data = genes) +
  geom_seq() +
  geom_gene()

Description

Draws the gene annotation labels on a chord diagram. This layer is independent from geom_gene(): add it after geom_gene() to annotate the gene arrows with their texts.

Usage

geom_gene_label(
  mapping = NULL,
  data = NULL,
  label_orientation = "horizontal",
  label_side = "outside",
  label_overlap = "hide",
  label_rotation = NULL,
  label_radial_offset = 0.04,
  label_circum_offset = NULL,
  label_circum_limit = NULL,
  label_wrap = NULL,
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

Details

This is the deterministic, fixed-position label layer. By default labels sit outside their sequence and labels that would collide are omitted in input-row order. Use label_overlap = "nudge" to retain the legacy gentle adjustment, or "allow" to draw every label at its requested position. For automatic arrangement with leader lines, use geom_gene_label_repel() instead.

Value

A ggplot2 layer. To let the labels avoid each other and the genes (with leader lines), use geom_gene_label_repel() instead.

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(gene_data_example)
genes <- gene_data_example |>
  transmute(accver, start, end, strand = source_strand, anno)
ggchord(seq_data = seqs, gene_data = genes) +
  geom_seq() +
  geom_gene() +
  geom_gene_label()

Description

Like geom_gene_label(), with deterministic external label placement. The default "radial" keeps horizontal text on a contour following each sequence; crowded names fan out along that contour. "auto" aligns left/right names in columns and uses radial placement elsewhere. "arc" rotates text along the sequence tangent.

Usage

geom_gene_label_repel(
  mapping = NULL,
  data = NULL,
  label_layout = "radial",
  label_wrap = NULL,
  label_fit = "wrap",
  label_max_lines = 2L,
  label_side = "outside",
  max_overlaps = Inf,
  label_segment_overlap = "fade",
  label_segment_overlap_alpha = 0.18,
  label_segment_linetype = "auto",
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  label_min_size = 1.5,
  ...
)

Arguments

Details

The local outside/inside label organisation adapts concepts used by SnapGene and Geneious. ggchord keeps generic mode names and integrates those ideas into its own geometry system. See SnapGene feature labels and Geneious label options.

Low-level force, padding, orientation and segment arguments used by earlier releases have been removed and now produce an error. Use label_layout for automatic placement, or geom_gene_label() for manual rotation and offsets.

Value

A ggplot2 layer that draws labels and leader lines together.

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(gene_data_example)
genes <- gene_data_example |>
  group_by(accver) |>
  slice_head(n = 2) |>
  ungroup() |>
  transmute(accver, start, end, strand = source_strand, anno)
ggchord(seq_data = seqs, gene_data = genes) +
  geom_seq() +
  geom_gene() +
  geom_gene_label_repel(label_wrap = 20)

Description

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

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

Value

A ggplot2 layer.

Examples

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)

Description

Draws alignment ribbons. Identity is mapped to ribbon_fill by default; When pident is absent, the default is a fixed grey fill with no Identity guide. Alignment length and identity are never inferred from endpoints. Alternative mappings and legends are controlled with aes(), ⁠scale_*()⁠ and guides().

Usage

geom_link_ribbon(
  mapping = NULL,
  data = NULL,
  link_ctrl_point = NULL,
  link_gap = NULL,
  link_avoid = c("uniform", "none", "smooth"),
  link_branch = c("none", "query", "subject"),
  link_branch_fraction = 0.15,
  fill = NULL,
  alpha = 0.42,
  colour = "#59636D",
  linewidth = 0.08,
  linetype = NULL,
  adjacent_only = NULL,
  pairs = NULL,
  position = "identity",
  show.legend = TRUE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A ggplot2 layer.

Examples

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)
ggchord(seq_data = seqs, ribbon_data = links) +
  geom_seq() +
  geom_link_ribbon()

Description

Primers are slender directional arcs drawn between the two lines of a double sequence backbone by default, not arrows in the feature stack. Add geom_primer_label_repel() for the matching unboxed label and leader.

Usage

geom_primer(
  mapping = NULL,
  data = NULL,
  side = c("between", "outside", "inside"),
  arc_offset = 0.045,
  arc_linewidth = 0.026,
  colour = "#A020F0",
  position = NULL,
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A ggplot2 layer.

Examples

library(dplyr)
data(plasmid_example_pUC19)
seqs <- plasmid_example_pUC19 |>
  select(accver, length)
primers <- find_primer_bindings(plasmid_example_pUC19, set = "universal")
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_primer(data = primers) +
  geom_primer_label_repel(data = primers) +
  coord_circular()

Description

Primer labels are unboxed, use the primer colour, and show one-based inclusive binding coordinates by default. Their leaders start at the directional primer arc's arrow tip (the primer 3-prime end). Factor start/end columns use their numeric labels for both displayed text and retained binding-coordinate metadata, matching feature geometry.

Usage

geom_primer_label_repel(
  mapping = NULL,
  data = NULL,
  side = c("outside", "inside"),
  show_location = TRUE,
  colour = "#A020F0",
  max_overlaps = Inf,
  position = NULL,
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A composite text and leader-line layer.

Description

Draw restriction sites, labels and deterministic leaders

Usage

geom_restriction_site(
  mapping = NULL,
  data = NULL,
  label = TRUE,
  label_style = c("enzyme_position", "enzyme", "position"),
  label_order = c("auto", "enzyme_position", "position_enzyme"),
  label_side = c("outside", "inside", "auto"),
  leader = c("radial", "elbow", "straight"),
  min_label_gap = NULL,
  tick_length = 0.04,
  label_offset = 0.18,
  colour = "#202020",
  linewidth = 0.28,
  label_size = 3.2,
  fontface = NULL,
  family = NULL,
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A ggplot2 layer.

See Also

ggchord_data_contract

Description

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

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

Value

A ggplot2 layer.

Examples

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

Description

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

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

Value

A ggplot2 layer. Other ggchord coordinate systems are unsupported.

Examples

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()

Description

Add a circular-sequence centre label

Usage

geom_seq_center_label(
  mapping = NULL,
  data = NULL,
  name = TRUE,
  length = TRUE,
  separator = "\n",
  name_style = list(),
  length_style = list(),
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A ggplot2 layer.

Description

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

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

Value

A ggplot2 layer.

Examples

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

Description

Draws rectangular bands on sequence arcs for one or more coordinate intervals. This is useful for marking loci, repeats, CRISPR arrays, or other user-defined regions without turning them into gene arrows.

Usage

geom_seq_region(
  mapping = NULL,
  data = NULL,
  fill = "#F59E0B",
  colour = "#B45309",
  alpha = 0.25,
  region_width = 0.08,
  region_offset = 0,
  region_side = c("inside", "outside", "auto"),
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

Value

A ggplot2 layer.

Examples

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)
region <- tibble(
  accver = links$qaccver[1], start = min(links$qstart[1], links$qend[1]),
  end = max(links$qstart[1], links$qend[1])
)
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_seq_region(data = region)

Description

Adds a free-standing reference bar in the empty space outside the sequence envelope. Its length uses the same bp-to-x conversion as every backbone in coord_collinear(), including independent windows on shared display rows. Display gaps are never interpreted as genomic length. Local reversals and original-source axis labels do not change the bar's bp scale. Chord and circular coordinates have local sequence axes instead and are rejected.

Usage

geom_seq_scale(
  mapping = NULL,
  data = NULL,
  length = NULL,
  label = NULL,
  location = c("bottomleft", "bottomright", "topleft", "topright"),
  offset = grid::unit(c(2, 6), "mm"),
  tick_height = grid::unit(1.5, "mm"),
  label_gap = grid::unit(1.5, "mm"),
  linewidth = 0.4,
  colour = "#3D4348",
  size = 3,
  position = "identity",
  show.legend = FALSE,
  inherit.aes = FALSE,
  ...
)

Arguments

Details

The bar does not claim to span one source interval. An explicit length can therefore exceed a single window and still be a valid distance reference in the shared linear metric. With no length, a small whole-number 1/2/5 reference is chosen from displayed window lengths. No source coordinates are modified and no missing genomic region is manufactured.

To change ticks and labels on sequence axes instead, use scale_seq_position_continuous(). A position scale configures existing axes; this geom adds an independent distance reference.

Value

One independent ggplot2 layer. Exported axis geometry retains the bp length, input row and measurement status for each bar.

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
ggchord(seq_data = seqs) +
  geom_seq() +
  coord_collinear() +
  geom_seq_scale(length = 10000)

Description

Tile and bar layers require accver, start, end; lines require accver and pos. Map track_value for numeric height and track_fill or track_colour for visual mapping. Values are never inferred from column names. group separates line series; positions must increase strictly within each sequence/series. NA height breaks lines or omits bars, never becomes zero. Inf is rejected. Tiles may overlap in input drawing order; no averaging, interpolation or implicit aggregation is performed.

Usage

geom_track_tile(
  mapping = NULL,
  data = NULL,
  position,
  fill = "#86AFB9",
  colour = NA,
  alpha = 1,
  linewidth = 0.25,
  linetype = 1,
  bounds = c("error", "clip"),
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

geom_track_line(
  mapping = NULL,
  data = NULL,
  position,
  colour = "#387D88",
  alpha = 1,
  linewidth = 0.4,
  linetype = 1,
  closed = FALSE,
  bounds = c("error", "clip"),
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

geom_track_bar(
  mapping = NULL,
  data = NULL,
  position,
  baseline = 0,
  fill = "#86AFB9",
  colour = NA,
  alpha = 1,
  linewidth = 0.25,
  linetype = 1,
  bounds = c("error", "clip"),
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

Arguments

Details

All coordinates are window-local, one-based inclusive. Interval bins occupy their full end - start + 1 bases, including one-base bins; line samples use the specified positions without binning.

Use focus_ggchord_track() for source windows. Lines never connect distinct windows, even when they share a display row. Circular lines close only with explicit closed = TRUE; missing endpoints are not joined across NA.

Value

A ggplot2 layer with independent input and a shared named band.

Examples

library(ggchord)
library(dplyr)
data(plasmid_example_pUC19)
track_seq <- plasmid_example_pUC19 |>
  select(accver, length)
starts <- seq.int(1L, track_seq$length, by = 100L)
gc_fraction <- function(sequence) {
  bases <- strsplit(sequence, "")[[1]]
  mean(bases %in% c("G", "C"))
}
bins <- tibble(
  accver = track_seq$accver,
  start = starts,
  end = pmin(starts + 99L, track_seq$length)
) |>
  rowwise() |>
  mutate(gc = gc_fraction(substr(plasmid_example_pUC19$sequence, start, end))) |>
  ungroup()
doc_theme <- theme_ggchord_publication(
  axis.text = element_text(size = 9), axis.text.check.overlap = TRUE
) +
  theme(legend.position = "bottom")
p_tracks <- ggchord(seq_data = track_seq) +
  geom_seq() +
  geom_seq_center_label() +
  geom_track_bar(aes(track_value = gc, track_fill = gc),
    data = bins,
    position = position_track("gc", width = unit(6, "mm"))
  ) +
  scale_track_value_continuous("gc", limits = c(0, 1), unit = "GC fraction") +
  scale_track_fill_gradientn("gc", colours = c("#EDF1EA", "#8AAE9C", "#345F58")) +
  coord_circular() +
  doc_theme

Description

Returns the layout owned by an explicit ggchord plot. This avoids ambiguous cross-talk when several plots are built in one R session. For layer-aware tabular results, prefer export_ggchord_layout(). See ggchord_layout_contract for fields, units and cache ownership. Device/context changes invalidate cached estimates, including ordinary label layouts. build = FALSE then reports that no current layout is cached.

Usage

get_chord_layout(plot, build = TRUE)

Arguments

Value

A chord layout list containing the computed geometry (sequence arcs, ribbon polygons, gene arrows, axis elements, extremes, colors, etc.)

Examples

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

Description

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

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

Arguments

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

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)

Description

The v0.16.4 API candidate consolidates the plotting, data and output contracts established in v0.16.1–v0.16.3. Candidate freezing is a development baseline, not a claim of v1.0.0 compatibility or complete platform/device validation. Correctness fixes remain possible with documented evidence and migration.

Plotting responsibilities

ggchord() supplies reference sequences and optional default input tables. Each layer retains its own data, mapping, parameters and identity. aes() selects data roles, scales control mapping rules/guides, geoms draw entities, Positions place them locally, coords select the canvas mode, and themes control non-data appearance. Explicit fixed styles take precedence over matching mappings; omit a fixed argument to retain its mapping. User scales take precedence over automatically inferred defaults.

geom_gene() remains the strictly directed gene shortcut over the generic geom_feature() constructor. Unknown-strand features remain unknown and use the generic feature entrance. The plasmid shortcut retains its distinct defaults. Fixed feature shape is shape; mapped shape is feature_shape. Gene/feature widths use width, label controls use ⁠label_*⁠, and point/area links use link_gap and link_ctrl_point. These names do not merge the distinct geometries or their defaults.

Chord, circular and collinear remain separate coordinate modes. Circular maps reject inter-sequence links; collinear maps reject circular-only restriction/primer/centre-label layers. geom_seq_scale() is a collinear bp reference bar; scale_seq_position_continuous() configures genomic axes. A matching name never implies that every geom supports every coord.

Names and migration errors

The colour spelling is preferred in documentation; existing color spelling aliases remain supported. Selected ggplot2/grid reexports retain the original upstream object and follow that dependency's public contract. Their internals and future upstream signatures are not frozen by ggchord.

Retired arguments remain errors with replacement guidance; they do not execute compatibility code. In v0.16.1, fixed feature_shape, old width, label and ribbon endpoint names were removed in favour of the names above. gene_offset/feature_offset were also removed then; use position = position_strand(offset = ...). Explicit strand-named offsets are signed, so negate the former minus-strand magnitude when migrating it. The old v1.0.0 removal deadline no longer applies.

Automatic gene/feature labels own their rotation, offsets, orientation and overlap policy. Manual label_rotation, label_radial_offset, label_circum_offset, label_circum_limit, label_orientation and label_overlap supplied through their ... now fail rather than being ignored. Use geom_gene_label() or geom_feature_label() for manual placement, or choose automatic geometry with label_layout. The old "aligned" label request becomes label_layout = "auto"; restriction leader = "trunk" becomes leader = "radial".

Constructor unknown arguments stop. Ordinary geom, scale, guide and theme extras retain their documented forwarding and upstream error/warning rules; there is no promise that all unknown names fail uniformly. Geometric roles must be evaluated before layout, whereas supported visual mappings may use after_stat()/after_scale(). Unknown legacy label prefixes never imply that a similarly named replacement parameter exists.

Data, units and results

Input accver and query/subject identifiers are preserved without adding or removing versions. Biological strand, display orientation and link direction remain distinct. Coordinates are one-based inclusive bp after explicit external-format adaptation. Missing values, defaults and NULL are defined per responsibility, not by one package-wide coercion rule. Standalone cleaning defaults to sorting reversed endpoints; preparation retains direction by default. Readers retain file/files with shared path expansion. See ggchord_data_contract for source rows, optional dependencies, transformations, aggregation estimates and search limits.

Native layout distances, bp, angles, numerical track domains and physical mm are separate quantities. Track IDs share numerical domains and consistent band declarations; their physical placement is not a numeric value scale. Existing documented return members remain supported. Prefer export_ggchord_layout() for layer-aware tables; get_chord_layout() remains available for the complete layout. Preview paths and target-size diagnostic reports retain separate purposes. See ggchord_layout_contract for stable fields, provenance, measurement status and plot/render cache ownership.

See Also

ggchord_data_contract, ggchord_layout_contract

Examples

library(dplyr)
data(plasmid_example_pUC19)
seqs <- plasmid_example_pUC19 |>
  select(accver, length)
feature_source <- find_common_features(plasmid_example_pUC19)
features <- feature_source |>
  select(accver, start, end, strand, type, anno)
# ASCII display copy for the default PDF help-example device.
features <- features |>
  mutate(anno = gsub("\u03b1", "alpha", anno, fixed = TRUE))
p <- ggchord(seq_data = seqs) +
  geom_seq() +
  geom_feature(data = features) +
  coord_circular()
export_ggchord_layout(p, include = "feature")$metadata$coordinate

Description

ggchord separates reading, adaptation, validation, explicit cleaning and preparation. None of these steps runs BLAST, infers a missing full sequence length from features, verifies homology experimentally, or adds plot layers.

Details

Read

The six read_*() functions parse local files. Both file and files accept path vectors and glob patterns. When both are supplied, file precedes files; matches expand in pattern order, and each normalized path is read once, retaining its first supplied spelling. Missing, empty, unmatched or directory paths fail. Text input must be UTF-8 (an initial BOM is accepted by table readers). Convert other encodings explicitly before reading. Import attributes record format, files and output counts. Tabular readers and FASTA lengths retain physical .source_line; optional .source_file gives row-level file identity. GenBank instead retains record/feature indices and source text in its report. Malformed field counts stop, rather than shifting fields between rows. Numeric conversion problems in BLAST/GFF3 warn and retain missing values for inspection and validation.

Adapt

as_ggchord_*() accepts documented tables or optional interval/sequence objects. Required IDs and positive integral coordinates are checked immediately; zero-based tables must be converted explicitly. Metadata name collisions receive prefixes and a column map. Required coordinate NA is an error, while unrelated metadata NA survives. Seqinfo, object metadata, names and upstream provenance are retained in the conversion attribute. Optional packages are never installed automatically.

Validate

validate_ggchord_data() reports all collected issues without changing input. strict = TRUE stops after collection if errors exist. Logical argument errors stop immediately. This validator describes constructor seq/ribbon/gene tables; generic unknown-strand features belong in preparation's named feature collections. Coordinate checks do not prove an alignment or a biological annotation.

Clean

clean_ggchord_data() explicitly applies selected policies and reports original rows and old/new values. Its historical reversed_interval = "sort" is retained; use "keep" for directional links or circular-origin features. Sorting cannot recover their original meaning later. Unknown-ID "keep" is an audit policy, not a guarantee that the result is drawable. NULL means an absent optional table, and an empty table remains a table.

Prepare

prepare_ggchord_data() adapts first, validates, then runs only requested steps in the documented order. Its cleaning default is reversed_interval = "keep", because downstream operations use endpoint directions. Adaptation errors therefore occur before cleaning; clean/drop malformed IDs separately when needed. Named features/links remain independent collections. Reports distinguish stage-local rows from composed original ribbon source sets.

Coordinates and direction

Genomic intervals are one-based inclusive: start == end is one base. The explicit adapters enforce integral coordinates. Legacy constructor validation, cleaning and raw focus accept finite numeric positions; their success alone does not certify integral genomic coordinates. Prefer integral windows for biological data and use adapters before these legacy entries when strict integer checks are required. BED/PAF half-open [a,b) becomes [a+1,b]; zero-width records cannot become nonempty intervals and are rejected. Link endpoint order can encode relative direction; it is not a circular-origin join. Feature start > end is context-dependent: circular plotting can split an origin join, while linear window workflows require explicit ordered segments and an envelope. A raw focus locus uses min/max of its bounds, not an origin wrap. strand is biological annotation, orientation is display choice, and link direction is relative. Single-base link endpoints have no order: supplied strand or relative direction can provide evidence, otherwise direction remains unknown. Merge and bundle retain these rows independently instead of manufacturing aggregate endpoint directions. Unknown orientation is kept separate from known direction in density and deduplication. Unknown strands remain unknown in adapters; GFF3's explicit legacy unstranded = "plus" is an exception, with source_strand retained. Prefer unstranded = "keep" and generic feature layers when direction is unknown.

Plotting uses a continuous display axis, not a base-cell raster: feature/axis chord anchors use pos/length, point-link anchors use (pos-1)/length. These historical graphical offsets do not change stored coordinates. Single-base features can use a point or widened glyph. No new endpoint convention is imposed on plots in this data-workflow revision.

Selection, projection and aggregation

Focus crops all selected tables and composes earliest source coordinates. Overlapping windows can copy a row. Ribbon clipping interpolates an endpoint correspondence, rounds to bp and marks estimated length; identity is retained, not recalculated. Segment preparation creates separate windows and explicit gaps; it never concatenates their biological sequences. Position mapping is invertible within the selected linear window and rejects segmented gaps. CDS projection uses observed complete codons and explicit phase/partial policies; it does not translate with the stored genetic-code ID. Protein identity/length remain source-prefixed metadata when links are projected.

Filtering retains full rows. Deduplication selects representatives and reports discarded rows; it does not combine their statistics. Merge creates envelopes and reports source sets, lengths and identities. Bundle groups by pair, relative endpoint direction and midpoint bins; both endpoints may be reversed together in one group. Envelope endpoints follow the first row's absolute direction. Bundle length is a rounded length-weighted mean of source lengths, identity is a length-weighted mean, and conflicting extra metadata become typed NA. These summaries are not new alignments. Supply group_by for metadata that must remain separate. Density retains every input row and measures bin weight relative to that pair's maximum bin; it is not coverage or statistical probability. Optimization suggests display order/orientation without changing biological strand or query/subject roles.

Search helpers

Cluster links use declared membership, with explicit paralog and segment policies, not sequence alignment. Primer exact and three-prime suffix searches report zero mismatches; a partial suffix is not full-oligo validation. Wallace temperature is a simple composition estimate, not an experimental prediction. Restriction results are motif matches and source-backed cut offsets; missing cuts remain unknown. Methylation status uses supplied/reference context and a limited sensitivity catalogue, not a complete digestion model. Linear context never wraps sequence ends. Common-feature confidence is a deterministic heuristic rank, not a probability or experimental confirmation. Its six-frame protein search uses the standard codon table without alternative starts, splicing or circular-origin protein matches. Source geneticCode metadata is not interpreted as a selectable translation table. Use exact DNA mode or an external code-aware analysis for nonstandard translation.

See Also

prepare_ggchord_data, read_genbank, as_ggchord_feature, project_ggchord_links

Description

export_ggchord_layout() is the recommended interface for consuming layer-aware geometry tables. get_chord_layout() retains the complete layout list and its documented geometry, bounds, colour and label members. Neither entrance is deprecated. view_ggchord() returns a temporary image path; diagnose_ggchord() returns evidence for one requested render.

Geometry and provenance

Selected export components are data frames; absent components may be empty data frames without columns. Nonempty geometry has layer_id, component and source_row. An ID identifies one layer occurrence in that plot; editing/reordering layers can change IDs. A source row indexes the resolved input for that layer/component, not necessarily a physical file line. Generated decorations use missing source rows. Aggregates may carry source_rows membership instead of identifying one observation. original_data = TRUE includes resolved inputs for selected nonempty components, after role mapping and input adaptation. It is not a raw-file archive. File line/record provenance and conversion attributes retain their separate meanings from ggchord_data_contract.

Cartesian geometry and bounding boxes use native layout data units. Genomic source coordinates remain one-based inclusive bp; they are not converted to Cartesian distances. Angles use degrees except explicitly internal sequence-reference angles. Text sizes use mm. Metadata retains coordinate_space, units, coordinate, rotation, rotation_applied, coord_transform_applied, ratio, fit, xlim, ylim and clip. Exported coordinates already include layout rotation, before the ggplot2 coord transform. Native data units are not millimetres or genomic bp.

Coordinate-specific tables

Circular annotation_registry retains its documented identity, owner, component/source row, inner track/radius/width/boundaries, outer region, sector, band, dominant band, slot, spill reason, crossing count, bounding box and leader corridor fields. Radii, widths and boxes use layout data units; tracks/slots are build-local resource indices. Missing values denote fields that do not apply. These resources are distinct from named quantitative track IDs and Position lanes.

Collinear sequence_layout retains reversible window/source origins, horizontal range, backbone y, display orientation, units per bp, x offset and anchor. Segmented rows also retain row/window order, breaks and display gap_bp; omitted gaps have no source mapping. orientation_diagnostics, connection_report and label_diagnostics retain support, selection and placed/hidden-label evidence, including layer/row provenance where applicable.

track_registry retains track ID, accession, placement, source layers, numerical limits in original value units, optional unit, domain status and measurement status. Native offsets/widths use layout units; ⁠_mm⁠ fields are physical mm contributions. normal_min/normal_max use layout units. track_diagnostics records input rows, retention/reason, coordinate clipping and the original bar baseline. axis_selection records selected sequence axes. label_fit_diagnostics retains original text, requested, minimum/final sizes in mm and fallback/hiding reasons. Empty diagnostic tables need not have a fixed column prototype.

Measurement and cache scope

render_context and diagnostic measurement distinguish estimated, unavailable and measured panel status. panel_mm, canvas_mm and, when measured, panel_bounds_mm use physical mm. units_per_mm and axis_units_per_inch convert layout units along x/y; units_per_inch is a conservative scalar text metric. geometry_metric_status and converged describe refinement accuracy separately from panel measurement. Estimated contexts can have missing dimensions and convergence. Device/basis/font conditions state the source and limits of the evidence. Refinement counts and private solver/candidate/cache structures are implementation details.

A plot composition owns a fresh layout cache; a build/getter may populate it. Device/context changes invalidate estimates, even for ordinary labels. get_chord_layout(build = FALSE) requires a current cache. Previews and diagnostics render independent copies and preserve the source cache. Reference-path reuse lasts only for one geometry calculation. Temporary render contexts restore their predecessor on normal or exceptional exit. Ordinary R assignment retains ggplot2 reference semantics for ggproto objects; arbitrary direct mutation of shared layer environments is not tracked as a new plot composition.

Stability and diagnostic limits

Existing documented members above remain supported. Additional columns may be attached for input metadata or geometry-specific needs; consumers should select named fields, not fixed column positions/counts. Numeric layouts can change with size, device, font and legitimate collision handling. Resource numbers and diagnostic reason details are not persistent biological IDs. No candidate layout, private cache or iteration count is a stable result.

Diagnostics retain measurement, checks, text, guides, colour_suggestions, label_diagnostics, annotation_registry, track_registry, track_diagnostics and warnings. Text/guide bounds and line/text sizes use mm; colour distances use the named model in each row. A measured panel does not certify collision-free geometry, font embedding, fallback, arbitrary grobs or cross-application portability. Preview paths live in a temporary directory and may be removed by cleanup; use ordinary ggplot2::ggsave() to keep a final file.

See Also

ggchord_data_contract, export_ggchord_layout(), get_chord_layout(), view_ggchord(), diagnose_ggchord()

Examples

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
p <- ggchord(seq_data = seqs) +
  geom_seq()
geometry <- export_ggchord_layout(p, include = "seq")
geometry$seq |>
  distinct(layer_id, component, source_row)

Description

ggchord re-exports a deliberately small set of ggplot2 helpers that are directly useful when constructing, annotating, styling, or saving a chord plot. Cartesian geoms, coordinates, facets, generic scales, and complete theme presets remain in ggplot2 so IDE completion stays focused.

Usage

aes(x, y, ...)

after_stat(x)

after_scale(x)

annotate(
  geom,
  x = NULL,
  y = NULL,
  xmin = NULL,
  xmax = NULL,
  ymin = NULL,
  ymax = NULL,
  xend = NULL,
  yend = NULL,
  ...,
  na.rm = FALSE
)

labs(
  ...,
  title = waiver(),
  subtitle = waiver(),
  caption = waiver(),
  tag = waiver(),
  dictionary = waiver(),
  alt = waiver(),
  alt_insight = waiver()
)

ggtitle(label, subtitle = waiver())

guides(...)

theme(
  ...,
  line,
  rect,
  text,
  title,
  point,
  polygon,
  geom,
  spacing,
  margins,
  aspect.ratio,
  axis.title,
  axis.title.x,
  axis.title.x.top,
  axis.title.x.bottom,
  axis.title.y,
  axis.title.y.left,
  axis.title.y.right,
  axis.text,
  axis.text.x,
  axis.text.x.top,
  axis.text.x.bottom,
  axis.text.y,
  axis.text.y.left,
  axis.text.y.right,
  axis.text.theta,
  axis.text.r,
  axis.ticks,
  axis.ticks.x,
  axis.ticks.x.top,
  axis.ticks.x.bottom,
  axis.ticks.y,
  axis.ticks.y.left,
  axis.ticks.y.right,
  axis.ticks.theta,
  axis.ticks.r,
  axis.minor.ticks.x.top,
  axis.minor.ticks.x.bottom,
  axis.minor.ticks.y.left,
  axis.minor.ticks.y.right,
  axis.minor.ticks.theta,
  axis.minor.ticks.r,
  axis.ticks.length,
  axis.ticks.length.x,
  axis.ticks.length.x.top,
  axis.ticks.length.x.bottom,
  axis.ticks.length.y,
  axis.ticks.length.y.left,
  axis.ticks.length.y.right,
  axis.ticks.length.theta,
  axis.ticks.length.r,
  axis.minor.ticks.length,
  axis.minor.ticks.length.x,
  axis.minor.ticks.length.x.top,
  axis.minor.ticks.length.x.bottom,
  axis.minor.ticks.length.y,
  axis.minor.ticks.length.y.left,
  axis.minor.ticks.length.y.right,
  axis.minor.ticks.length.theta,
  axis.minor.ticks.length.r,
  axis.line,
  axis.line.x,
  axis.line.x.top,
  axis.line.x.bottom,
  axis.line.y,
  axis.line.y.left,
  axis.line.y.right,
  axis.line.theta,
  axis.line.r,
  legend.background,
  legend.margin,
  legend.spacing,
  legend.spacing.x,
  legend.spacing.y,
  legend.key,
  legend.key.size,
  legend.key.height,
  legend.key.width,
  legend.key.spacing,
  legend.key.spacing.x,
  legend.key.spacing.y,
  legend.key.justification,
  legend.frame,
  legend.ticks,
  legend.ticks.length,
  legend.axis.line,
  legend.text,
  legend.text.position,
  legend.title,
  legend.title.position,
  legend.position,
  legend.position.inside,
  legend.direction,
  legend.byrow,
  legend.justification,
  legend.justification.top,
  legend.justification.bottom,
  legend.justification.left,
  legend.justification.right,
  legend.justification.inside,
  legend.location,
  legend.box,
  legend.box.just,
  legend.box.margin,
  legend.box.background,
  legend.box.spacing,
  panel.background,
  panel.border,
  panel.spacing,
  panel.spacing.x,
  panel.spacing.y,
  panel.grid,
  panel.grid.major,
  panel.grid.minor,
  panel.grid.major.x,
  panel.grid.major.y,
  panel.grid.minor.x,
  panel.grid.minor.y,
  panel.ontop,
  panel.widths,
  panel.heights,
  plot.background,
  plot.title,
  plot.title.position,
  plot.subtitle,
  plot.caption,
  plot.caption.position,
  plot.tag,
  plot.tag.position,
  plot.tag.location,
  plot.margin,
  strip.background,
  strip.background.x,
  strip.background.y,
  strip.clip,
  strip.placement,
  strip.text,
  strip.text.x,
  strip.text.x.bottom,
  strip.text.x.top,
  strip.text.y,
  strip.text.y.left,
  strip.text.y.right,
  strip.switch.pad.grid,
  strip.switch.pad.wrap,
  complete = FALSE,
  validate = TRUE
)

element_blank()

element_line(
  colour = NULL,
  linewidth = NULL,
  linetype = NULL,
  lineend = NULL,
  color = NULL,
  linejoin = NULL,
  arrow = NULL,
  arrow.fill = NULL,
  inherit.blank = FALSE,
  size = deprecated(),
  ...
)

element_rect(
  fill = NULL,
  colour = NULL,
  linewidth = NULL,
  linetype = NULL,
  color = NULL,
  linejoin = NULL,
  inherit.blank = FALSE,
  size = deprecated(),
  ...
)

element_text(
  family = NULL,
  face = NULL,
  colour = NULL,
  size = NULL,
  hjust = NULL,
  vjust = NULL,
  angle = NULL,
  lineheight = NULL,
  color = NULL,
  margin = NULL,
  debug = NULL,
  inherit.blank = FALSE,
  ...
)

margin(t = 0, r = 0, b = 0, l = 0, unit = "pt", ...)

rel(x)

ggsave(
  filename,
  plot = get_last_plot(),
  device = NULL,
  path = NULL,
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL,
  create.dir = FALSE,
  ...
)

last_plot()

waiver()

expansion(mult = 0, add = 0)

position_identity()

PositionIdentity

Arguments

Details

Mapping helpers are aes(), after_stat() and after_scale(); ggplot2::stage() combines stages of one aesthetic. Use labs() and ggtitle() for titles, guides() for guide selection, and theme() with the element_*() helpers for appearance. annotate() adds fixed annotations. margin() and rel() specify theme sizes; waiver() and expansion() specify automatic or expanded scale settings. position_identity() and PositionIdentity are the upstream identity placement helpers. ggsave() saves a supplied plot; last_plot() retrieves ggplot2's last plot. Each symbol is the original ggplot2 function or object, and can also be called with its ggplot2:: namespace. unit() and arrow() come from grid.

Description

These are the original grid functions, available after loading ggchord. Use physical units for theme spacing and arrows for point links.

Usage

unit(x, units, data = NULL)

arrow(angle = 30, length = unit(0.25, "inches"), ends = "last", type = "open")

Arguments

Value

A grid unit or arrow object.

Examples

unit(2, "mm")
arrow(length = unit(2, "mm"), type = "closed")

Description

Thin wrappers around ggplot2::guide_legend() and ggplot2::guide_colourbar() with compact defaults suitable for chord diagrams. All ordinary ggplot2 guide arguments remain available.

Usage

guide_ggchord_legend(
  title = ggplot2::waiver(),
  theme = NULL,
  position = NULL,
  direction = NULL,
  override.aes = list(),
  nrow = NULL,
  ncol = NULL,
  reverse = FALSE,
  order = 0,
  size_scale = 1,
  ...
)

guide_ggchord_colourbar(
  title = ggplot2::waiver(),
  theme = NULL,
  nbin = NULL,
  display = "raster",
  alpha = NA,
  draw.ulim = TRUE,
  draw.llim = TRUE,
  angle = NULL,
  position = NULL,
  direction = NULL,
  reverse = FALSE,
  order = 0,
  available_aes = c("colour", "color", "fill", "ribbon_fill", "gene_fill",
    "feature_fill", "region_fill"),
  size_scale = 1,
  ...
)

guide_ggchord_colorbar(
  title = ggplot2::waiver(),
  theme = NULL,
  nbin = NULL,
  display = "raster",
  alpha = NA,
  draw.ulim = TRUE,
  draw.llim = TRUE,
  angle = NULL,
  position = NULL,
  direction = NULL,
  reverse = FALSE,
  order = 0,
  available_aes = c("colour", "color", "fill", "ribbon_fill", "gene_fill",
    "feature_fill", "region_fill"),
  size_scale = 1,
  ...
)