Layered Chord, Circular and Linear Sequence Visualization

Documentation for package ‘ggchord’ version 0.16.6

Help Pages

-- A --

aes	Selected ggplot2 helpers for ggchord plots
after_scale	Selected ggplot2 helpers for ggchord plots
after_stat	Selected ggplot2 helpers for ggchord plots
annotate	Selected ggplot2 helpers for ggchord plots
arrow	Physical units and direction arrows
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

-- B --

build_ggchord_cds	Build an explicit spliced CDS coordinate map
bundle_ggchord_ribbons	Bundle dense alignment ribbons explicitly

-- C --

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

-- D --

deduplicate_ggchord_ribbons	Deduplicate alignment ribbons
diagnose_ggchord	Inspect one target-size render without changing the plot

-- E --

element_blank	Selected ggplot2 helpers for ggchord plots
element_line	Selected ggplot2 helpers for ggchord plots
element_rect	Selected ggplot2 helpers for ggchord plots
element_text	Selected ggplot2 helpers for ggchord plots
expansion	Selected ggplot2 helpers for ggchord plots
export_ggchord_layout	Export computed ggchord geometry

-- F --

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

-- G --

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_bar	Draw explicit quantitative tracks along sequence backbones
geom_track_line	Draw explicit quantitative tracks along sequence backbones
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
ggsave	Selected ggplot2 helpers for ggchord plots
ggtitle	Selected ggplot2 helpers for ggchord plots
grid-helpers	Physical units and direction arrows
guides	Selected ggplot2 helpers for ggchord plots
guide_ggchord_colorbar	Guides for ggchord role aesthetics
guide_ggchord_colourbar	Guides for ggchord role aesthetics
guide_ggchord_legend	Guides for ggchord role aesthetics

-- L --

labs	Selected ggplot2 helpers for ggchord plots
last_plot	Selected ggplot2 helpers for ggchord plots
link_ggchord_clusters	Convert explicit homology-cluster membership to feature links

-- M --

map_ggchord_position	Convert genomic positions to or from a linear ggchord layout
margin	Selected ggplot2 helpers for ggchord plots
merge_ggchord_ribbons	Merge adjacent or overlapping alignment blocks of the same sequence pair

-- O --

optimize_ggchord_layout

Optimize sequence order and orientation for ribbon readability

-- P --

plasmid_example_pBluescript_II_SK_plus	Circular plasmid sequence examples
plasmid_example_pBR322	Circular plasmid sequence examples
plasmid_example_pCAMBIA1300	Circular plasmid sequence examples
plasmid_example_pcDNA3_1_plus	Circular plasmid sequence examples
plasmid_example_pDONR221	Circular plasmid sequence examples
plasmid_example_pEarleyGate_201	Circular plasmid sequence examples
plasmid_example_pETDuet_1	Circular plasmid sequence examples
plasmid_example_pET_28a_plus	Circular plasmid sequence examples
plasmid_example_pSB1C3	Circular plasmid sequence examples
plasmid_example_pSpCas9_BB_2A_GFP_PX458	Circular plasmid sequence examples
plasmid_example_pTRE_Tight_BI	Circular plasmid sequence examples
plasmid_example_pTRIPZ	Circular plasmid sequence examples
plasmid_example_pUC19	Circular plasmid sequence examples
plasmid_example_pUC19c	Circular plasmid sequence examples
PositionIdentity	Selected ggplot2 helpers for ggchord plots
position_feature_stack	Stack overlapping genes or features on local lanes
position_identity	Selected ggplot2 helpers for ggchord plots
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

-- R --

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
rel	Selected ggplot2 helpers for ggchord plots
restriction_site_example	Restriction sites for the minimal single-genome fixture
ribbon_data_example	Example alignment data

-- S --

scale_feature_fill_manual	Gene, feature and region fill scales
scale_feature_fill_plasmid	Plasmid-map feature presets
scale_feature_shape_manual	Feature shape scale
scale_feature_shape_plasmid	Plasmid-map feature presets
scale_gene_fill_manual	Gene, feature and region fill scales
scale_link	Scales for point links
scale_link_alpha_continuous	Scales for point links
scale_link_alpha_manual	Scales for point links
scale_link_color_gradientn	Scales for point links
scale_link_color_manual	Scales for point links
scale_link_colour_gradientn	Scales for point links
scale_link_colour_manual	Scales for point links
scale_link_linetype_manual	Scales for point links
scale_link_linewidth_continuous	Scales for point links
scale_link_linewidth_manual	Scales for point links
scale_region_fill_manual	Gene, feature and region fill scales
scale_ribbon_alpha_continuous	Ribbon alpha, outline and linetype scales
scale_ribbon_alpha_manual	Ribbon alpha, outline and linetype scales
scale_ribbon_color_manual	Ribbon alpha, outline and linetype scales
scale_ribbon_colour_manual	Ribbon alpha, outline and linetype scales
scale_ribbon_fill_gradientn	Ribbon fill scales
scale_ribbon_fill_identity	Ribbon fill scales
scale_ribbon_fill_manual	Ribbon fill scales
scale_ribbon_fill_stepsn	Ribbon fill scales
scale_ribbon_linetype_manual	Ribbon alpha, outline and linetype scales
scale_seq_color_manual	Sequence colour 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_colour_gradientn	Set a track's fill or colour mapping
scale_track_colour_manual	Set a track's fill or colour mapping
scale_track_fill_gradientn	Set a track's fill or colour mapping
scale_track_fill_manual	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

-- T --

theme	Selected ggplot2 helpers for ggchord plots
theme_ggchord	ggchord themes
theme_ggchord_dark	ggchord themes
theme_ggchord_minimal	ggchord themes
theme_ggchord_plasmid	ggchord themes
theme_ggchord_publication	ggchord themes

-- U --

unit	Physical units and direction arrows

-- V --

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

-- W --

waiver

Selected ggplot2 helpers for ggchord plots

-- misc --

+.ggchord

Combine a ggchord plot with ggplot2 objects