+.ggchord               Combine a ggchord plot with ggplot2 objects
as.data.frame.ggchord_validation
                        Coerce a validation result to a flat data.frame
as_ggchord_feature      Convert intervals to generic ggchord features
as_ggchord_link         Convert paired genomic intervals to ggchord
                        links
as_ggchord_seq          Convert sequence information to ggchord input
build_ggchord_cds       Build an explicit spliced CDS coordinate map
bundle_ggchord_ribbons
                        Bundle dense alignment ribbons explicitly
clean_ggchord_data      Clean ggchord input data with explicit,
                        report-driven policies
coord_chord             Chord diagram coordinate system
coord_circular          Single-sequence circular coordinate system
coord_collinear         Linear multi-sequence collinearity coordinates
deduplicate_ggchord_ribbons
                        Deduplicate alignment ribbons
diagnose_ggchord        Inspect one target-size render without changing
                        the plot
export_ggchord_layout   Export computed ggchord geometry
filter_ggchord_ribbons
                        Filter alignment ribbons before plotting
filter_restriction_sites
                        Filter restriction sites for display
find_common_features    Find common biological features in DNA
                        sequences
find_ggchord_loci       Find genomic loci around explicitly identified
                        features
find_primer_bindings    Find sequencing-primer binding sites
find_restriction_sites
                        Find restriction pattern matches and cleavage
                        coordinates
focus_ggchord_data      Focus ggchord data on one or more loci
focus_ggchord_track     Focus quantitative intervals or samples without
                        bridging omitted windows
gene_data_example       Example gene annotation data
geom_feature            Draw generic genomic features
geom_feature_label      Label generic genomic features
geom_feature_label_repel
                        Automatically arrange generic feature labels
geom_feature_plasmid    Draw SnapGene-style features on a circular
                        plasmid
geom_gene               Add a gene arrow layer
geom_gene_label         Add a gene label layer
geom_gene_label_repel   Add an automatically arranged gene label layer
geom_link_line          Draw point-to-point sequence links
geom_link_ribbon        Add an alignment ribbon layer
geom_primer             Draw primer binding ranges on a circular
                        sequence
geom_primer_label_repel
                        Arrange primer labels and leaders
geom_restriction_site   Draw restriction sites, labels and
                        deterministic leaders
geom_seq                Add a sequence arc layer
geom_seq_break          Mark cropped ends of linear sequences
geom_seq_center_label   Add a circular-sequence centre label
geom_seq_label          Add a sequence label layer
geom_seq_region         Highlight regions along sequence arcs
geom_seq_scale          Add a shared base-pair scale bar to a linear
                        display
geom_track_tile         Draw explicit quantitative tracks along
                        sequence backbones
get_chord_layout        Get the chord layout from a ggchord plot
ggchord                 Layered chord, circular and collinear sequence
                        plots
ggchord_api_contract    Candidate API and migration contract
ggchord_data_contract   Data workflow and biological coordinate
                        contracts
ggchord_layout_contract
                        Layout results, units and ownership
ggplot2-helpers         Selected ggplot2 helpers for ggchord plots
grid-helpers            Physical units and direction arrows
guide_ggchord_legend    Guides for ggchord role aesthetics
link_ggchord_clusters   Convert explicit homology-cluster membership to
                        feature links
map_ggchord_position    Convert genomic positions to or from a linear
                        ggchord layout
merge_ggchord_ribbons   Merge adjacent or overlapping alignment blocks
                        of the same sequence pair
optimize_ggchord_layout
                        Optimize sequence order and orientation for
                        ribbon readability
plasmid_example_pUC19   Circular plasmid sequence examples
position_feature_stack
                        Stack overlapping genes or features on local
                        lanes
position_plasmid        Place both feature strands on one shared band
position_strand         Place features on opposite sides according to
                        strand
position_track          Place a quantitative layer in an explicit
                        sequence-local band
prepare_ggchord_data    Prepare named ggchord tables with an explicit
                        audit trail
primer_catalog          Inspect the bundled sequencing-primer catalogue
print.ggchord_clean     Print a cleaned ggchord data result
project_ggchord_features
                        Project protein domains or genomic features
                        through a spliced CDS map
project_ggchord_links   Project explicitly ungapped protein links to
                        genomic coding segments
read_bed                Read BED intervals as ggchord features
read_blast              Read one or more BLAST tabular output files
                        into ribbon_data format
read_fasta_lengths      Read one or more FASTA files into seq_data
                        format
read_genbank            Import local GenBank or GBFF records using an
                        optional mature parser
read_gff3               Read one or more GFF3 files into gene_data
                        format
read_paf                Read PAF mappings as ggchord links
restriction_site_example
                        Restriction sites for the minimal single-genome
                        fixture
ribbon_data_example     Example alignment data
scale_feature_fill_plasmid
                        Plasmid-map feature presets
scale_feature_shape_manual
                        Feature shape scale
scale_gene_fill_manual
                        Gene, feature and region fill scales
scale_link              Scales for point links
scale_ribbon_alpha_continuous
                        Ribbon alpha, outline and linetype scales
scale_ribbon_fill_stepsn
                        Ribbon fill scales
scale_seq_colour_manual
                        Sequence colour scales
scale_seq_position_continuous
                        Genomic sequence position scale
scale_seq_ring_manual   Explicit sequence ring scale
scale_track_fill_gradientn
                        Set a track's fill or colour mapping
scale_track_value_continuous
                        Set a named track's numerical height scale
segment_ggchord_data    Prepare independent windows for a segmented
                        linear display
seq_data_example        Example sequence data
single_gene_example     Minimal single-genome gene fixture
single_genome_example   Minimal single-genome sequence fixture
stat_ribbon_bundle      Bundle ribbons as a ggchord stat
stat_ribbon_density     Compute local ribbon density as a ggchord stat
theme_ggchord           ggchord themes
validate_ggchord_data   Validate ggchord input data before plotting
validate_ggchord_hierarchy
                        Validate explicit genome and contig
                        relationships
view_ggchord            Preview a ggchord plot at its intended export
                        size
