Package index • ggchord

Construction and contracts

coord_chord(): Chord diagram coordinate system
coord_circular(): Single-sequence circular coordinate system
coord_collinear(): Linear multi-sequence collinearity coordinates
ggchord(): Layered chord, circular and collinear sequence plots
ggchord_api_contract: Candidate API and migration contract
ggchord_layout_contract: Layout results, units and ownership

Input and validation

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
clean_ggchord_data(): Clean ggchord input data with explicit, report-driven policies
ggchord_data_contract: Data workflow and biological coordinate contracts
prepare_ggchord_data(): Prepare named ggchord tables with an explicit audit trail
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
validate_ggchord_data(): Validate ggchord input data before plotting
validate_ggchord_hierarchy(): Validate explicit genome and contig relationships

Geometry and labels

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

Positions, scales, themes and guides

guide_ggchord_legend() guide_ggchord_colourbar() guide_ggchord_colorbar(): Guides for ggchord role aesthetics
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
scale_feature_fill_plasmid() scale_feature_shape_plasmid(): Plasmid-map feature presets
scale_feature_shape_manual(): Feature shape scale
scale_gene_fill_manual() scale_feature_fill_manual() scale_region_fill_manual(): Gene, feature and region fill scales
scale_link_colour_manual() scale_link_color_manual() scale_link_alpha_manual() scale_link_linewidth_manual() scale_link_linetype_manual() scale_link_colour_gradientn() scale_link_color_gradientn() scale_link_alpha_continuous() scale_link_linewidth_continuous(): Scales for point links
scale_ribbon_alpha_continuous() scale_ribbon_alpha_manual() scale_ribbon_colour_manual() scale_ribbon_color_manual() scale_ribbon_linetype_manual(): Ribbon alpha, outline and linetype scales
scale_ribbon_fill_stepsn() scale_ribbon_fill_gradientn() scale_ribbon_fill_manual() scale_ribbon_fill_identity(): Ribbon fill scales
scale_seq_colour_manual() scale_seq_color_manual(): Sequence colour scales
scale_seq_position_continuous(): Genomic sequence position scale
scale_seq_ring_manual(): Explicit sequence ring scale
theme_ggchord() theme_ggchord_minimal() theme_ggchord_dark() theme_ggchord_publication() theme_ggchord_plasmid(): ggchord themes

Quantitative tracks

geom_track_tile() geom_track_line() geom_track_bar(): Draw explicit quantitative tracks along sequence backbones
position_track(): Place a quantitative layer in an explicit sequence-local band
scale_track_fill_gradientn() scale_track_fill_manual() scale_track_colour_gradientn() scale_track_colour_manual(): Set a track's fill or colour mapping
scale_track_value_continuous(): Set a named track's numerical height scale

Sequence recognition

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
primer_catalog(): Inspect the bundled sequencing-primer catalogue

Projection and comparison workflows

build_ggchord_cds(): Build an explicit spliced CDS coordinate map
bundle_ggchord_ribbons(): Bundle dense alignment ribbons explicitly
deduplicate_ggchord_ribbons(): Deduplicate alignment ribbons
filter_ggchord_ribbons(): Filter alignment ribbons before plotting
focus_ggchord_data(): Focus ggchord data on one or more loci
focus_ggchord_track(): Focus quantitative intervals or samples without bridging omitted windows
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
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
segment_ggchord_data(): Prepare independent windows for a segmented linear display
stat_ribbon_bundle(): Bundle ribbons as a ggchord stat
stat_ribbon_density(): Compute local ribbon density as a ggchord stat

Output and diagnostics

diagnose_ggchord(): Inspect one target-size render without changing the plot
export_ggchord_layout(): Export computed ggchord geometry
get_chord_layout(): Get the chord layout from a ggchord plot
optimize_ggchord_layout(): Optimize sequence order and orientation for ribbon readability
view_ggchord(): Preview a ggchord plot at its intended export size

Methods, teaching data and upstream reexports

as.data.frame(<ggchord_validation>): Coerce a validation result to a flat data.frame
gene_data_example: Example gene annotation data
aes() after_stat() after_scale() annotate() labs() ggtitle() guides() theme() element_blank() element_line() element_rect() element_text() margin() rel() ggsave() last_plot() waiver() expansion() position_identity() PositionIdentity: Selected ggplot2 helpers for ggchord plots
unit() arrow(): Physical units and direction arrows
plasmid_example_pUC19 plasmid_example_pUC19c plasmid_example_pBR322 plasmid_example_pBluescript_II_SK_plus plasmid_example_pCAMBIA1300 plasmid_example_pcDNA3_1_plus plasmid_example_pDONR221 plasmid_example_pEarleyGate_201 plasmid_example_pET_28a_plus plasmid_example_pETDuet_1 plasmid_example_pSB1C3 plasmid_example_pSpCas9_BB_2A_GFP_PX458 plasmid_example_pTRE_Tight_BI plasmid_example_pTRIPZ: Circular plasmid sequence examples
`+`(<ggchord>): Combine a ggchord plot with ggplot2 objects
print(<ggchord_clean>): Print a cleaned ggchord data result
restriction_site_example: Restriction sites for the minimal single-genome fixture
ribbon_data_example: Example alignment data
seq_data_example: Example sequence data
single_gene_example: Minimal single-genome gene fixture
single_genome_example: Minimal single-genome sequence fixture