Package: ggchord 0.16.7.9000

ggchord: Layered Chord, Circular and Linear Sequence Visualization

A 'ggplot2'-based package for multi-sequence alignment chord diagrams, linear collinearity plots and single circular sequence maps. A layered grammar combines sequence backbones, interval links, genes, general biological features, labels, quantitative tracks, genomic axes and restriction sites. Feature placement is expressed with reusable Position objects, while role-specific scales and themes keep data mapping separate from geometry and appearance.

Authors:Jem Dang [aut, cre]

ggchord_0.16.7.9000.tar.gz
ggchord_0.16.7.9000.zip(r-4.7-any)ggchord_0.16.7.9000.zip(r-4.6-any)ggchord_0.16.7.9000.zip(r-4.5-any)
ggchord_0.16.7.9000.tgz(r-4.6-any)ggchord_0.16.7.9000.tgz(r-4.5-any)
ggchord_0.16.7.9000.tar.gz(r-4.7-any)ggchord_0.16.7.9000.tar.gz(r-4.6-any)
ggchord_0.16.7.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggchord/json (API)

# Install 'ggchord' in R:
install.packages('ggchord', repos = c('https://dangjem.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dangjem/ggchord/issues

Datasets:

On CRAN:

Conda:

bioinformaticschord-diagramcomparative-genomicsgenome-annotationgenomics-visualizationggplot2plasmidsequence-alignmentsyntenysynteny-plot

6.78 score 13 stars 46 scripts 295 downloads 130 exports 17 dependencies

Last updated from:b4eaeb1bcc. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK249
source / vignettesOK262
linux-releaseOK216
macos-releaseOK236
macos-oldrelOK200
windows-develOK205
windows-releaseOK197
windows-oldrelOK148
wasm-releaseOK140

Exports:aesafter_scaleafter_statannotatearrowas_ggchord_featureas_ggchord_linkas_ggchord_seqbuild_ggchord_cdsbundle_ggchord_ribbonsclean_ggchord_datacoord_chordcoord_circularcoord_collineardeduplicate_ggchord_ribbonsdiagnose_ggchordelement_blankelement_lineelement_rectelement_textexpansionexport_ggchord_layoutfilter_ggchord_ribbonsfilter_restriction_sitesfind_common_featuresfind_ggchord_locifind_primer_bindingsfind_restriction_sitesfocus_ggchord_datafocus_ggchord_trackgeom_featuregeom_feature_labelgeom_feature_label_repelgeom_feature_plasmidgeom_genegeom_gene_labelgeom_gene_label_repelgeom_link_linegeom_link_ribbongeom_primergeom_primer_label_repelgeom_restriction_sitegeom_seqgeom_seq_breakgeom_seq_center_labelgeom_seq_labelgeom_seq_regiongeom_seq_scalegeom_track_bargeom_track_linegeom_track_tileget_chord_layoutggchordggsaveggtitleguide_ggchord_colorbarguide_ggchord_colourbarguide_ggchord_legendguideslabslast_plotlink_ggchord_clustersmap_ggchord_positionmarginmerge_ggchord_ribbonsoptimize_ggchord_layoutposition_feature_stackposition_identityposition_plasmidposition_strandposition_trackPositionIdentityprepare_ggchord_dataprimer_catalogproject_ggchord_featuresproject_ggchord_linksread_bedread_blastread_fasta_lengthsread_genbankread_gff3read_pafrelscale_feature_fill_manualscale_feature_fill_plasmidscale_feature_shape_manualscale_feature_shape_plasmidscale_gene_fill_manualscale_link_alpha_continuousscale_link_alpha_manualscale_link_color_gradientnscale_link_color_manualscale_link_colour_gradientnscale_link_colour_manualscale_link_linetype_manualscale_link_linewidth_continuousscale_link_linewidth_manualscale_region_fill_manualscale_ribbon_alpha_continuousscale_ribbon_alpha_manualscale_ribbon_color_manualscale_ribbon_colour_manualscale_ribbon_fill_gradientnscale_ribbon_fill_identityscale_ribbon_fill_manualscale_ribbon_fill_stepsnscale_ribbon_linetype_manualscale_seq_color_manualscale_seq_colour_manualscale_seq_position_continuousscale_seq_ring_manualscale_track_colour_gradientnscale_track_colour_manualscale_track_fill_gradientnscale_track_fill_manualscale_track_value_continuoussegment_ggchord_datastat_ribbon_bundlestat_ribbon_densitythemetheme_ggchordtheme_ggchord_darktheme_ggchord_minimaltheme_ggchord_plasmidtheme_ggchord_publicationunitvalidate_ggchord_datavalidate_ggchord_hierarchyview_ggchordwaiver

Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecycleR6RColorBrewerrlangS7scalesvctrsviridisLitewithr

ggchord: chord, collinear and plasmid tutorial
Download and install | Download and install | Source downloads | Optional dependencies | Confirm the installation | Next steps | Draw sequence backbones | Draw the backbones | Read the plot | Try removing the labels | Use your own sequences | Draw your first collinear plot | Draw four backbones | Read position and length on a common scale | Try removing the sequence names | Use your own sequences | Draw your first circular map | Draw the backbone and centre label | Read the ticks around the circle | Use your own sequence
Rendered fromggchord_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-11-05
Started: 2025-07-07

ggchord：弦图、共线性图与质粒图教程
下载与安装 | 下载与安装 | 源码下载 | 可选依赖 | 确认安装 | 下一步 | 绘制序列骨架 | 绘制骨架 | 读图 | 试着去掉标签 | 换成自己的序列 | 绘制共线性骨架 | 绘制四条骨架 | 按共同尺度读位置和长度 | 试着去掉序列名 | 换用自己的序列 | 绘制圆形骨架 | 绘制骨架与中心名称 | 读圆周刻度 | 换用自己的序列
Rendered fromggchord_guide_hans.Rmdusingknitr::rmarkdown

Last update: 2026-11-05
Started: 2026-08-14

Readme and manuals

Help Manual

Help pageTopics
Combine a ggchord plot with ggplot2 objects+.ggchord
Convert intervals to generic ggchord featuresas_ggchord_feature
Convert paired genomic intervals to ggchord linksas_ggchord_link
Convert sequence information to ggchord inputas_ggchord_seq
Coerce a validation result to a flat data.frameas.data.frame.ggchord_validation
Build an explicit spliced CDS coordinate mapbuild_ggchord_cds
Bundle dense alignment ribbons explicitlybundle_ggchord_ribbons
Clean ggchord input data with explicit, report-driven policiesclean_ggchord_data
Chord diagram coordinate systemcoord_chord
Single-sequence circular coordinate systemcoord_circular
Linear multi-sequence collinearity coordinatescoord_collinear
Deduplicate alignment ribbonsdeduplicate_ggchord_ribbons
Inspect one target-size render without changing the plotdiagnose_ggchord
Export computed ggchord geometryexport_ggchord_layout
Filter alignment ribbons before plottingfilter_ggchord_ribbons
Filter restriction sites for displayfilter_restriction_sites
Find common biological features in DNA sequencesfind_common_features
Find genomic loci around explicitly identified featuresfind_ggchord_loci
Find sequencing-primer binding sitesfind_primer_bindings
Find restriction pattern matches and cleavage coordinatesfind_restriction_sites
Focus ggchord data on one or more locifocus_ggchord_data
Focus quantitative intervals or samples without bridging omitted windowsfocus_ggchord_track
Example gene annotation datagene_data_example
Draw generic genomic featuresgeom_feature
Label generic genomic featuresgeom_feature_label
Automatically arrange generic feature labelsgeom_feature_label_repel
Draw SnapGene-style features on a circular plasmidgeom_feature_plasmid
Add a gene arrow layergeom_gene
Add a gene label layergeom_gene_label
Add an automatically arranged gene label layergeom_gene_label_repel
Draw point-to-point sequence linksgeom_link_line
Add an alignment ribbon layergeom_link_ribbon
Draw primer binding ranges on a circular sequencegeom_primer
Arrange primer labels and leadersgeom_primer_label_repel
Draw restriction sites, labels and deterministic leadersgeom_restriction_site
Add a sequence arc layergeom_seq
Mark cropped ends of linear sequencesgeom_seq_break
Add a circular-sequence centre labelgeom_seq_center_label
Add a sequence label layergeom_seq_label
Highlight regions along sequence arcsgeom_seq_region
Add a shared sequence-position scale bar to a linear displaygeom_seq_scale
Draw explicit quantitative tracks along sequence backbonesgeom_track_bar geom_track_line geom_track_tile
Get the chord layout from a ggchord plotget_chord_layout
Layered chord, circular and collinear sequence plotsggchord
Candidate API and migration contractggchord_api_contract
Data workflow and biological coordinate contractsggchord_data_contract
Layout results, units and ownershipggchord_layout_contract
Selected ggplot2 helpers for ggchord plotsaes after_scale after_stat annotate element_blank element_line element_rect element_text expansion ggplot2-helpers ggsave ggtitle guides labs last_plot margin PositionIdentity position_identity rel theme waiver
Physical units and direction arrowsarrow grid-helpers unit
Guides for ggchord role aestheticsguide_ggchord_colorbar guide_ggchord_colourbar guide_ggchord_legend
Convert explicit homology-cluster membership to feature linkslink_ggchord_clusters
Convert genomic positions to or from a linear ggchord layoutmap_ggchord_position
Merge adjacent or overlapping alignment blocks of the same sequence pairmerge_ggchord_ribbons
Optimize sequence order and orientation for ribbon readabilityoptimize_ggchord_layout
Circular plasmid sequence examplesplasmid_example_pBluescript_II_SK_plus plasmid_example_pBR322 plasmid_example_pCAMBIA1300 plasmid_example_pcDNA3_1_plus plasmid_example_pDONR221 plasmid_example_pEarleyGate_201 plasmid_example_pETDuet_1 plasmid_example_pET_28a_plus plasmid_example_pSB1C3 plasmid_example_pSpCas9_BB_2A_GFP_PX458 plasmid_example_pTRE_Tight_BI plasmid_example_pTRIPZ plasmid_example_pUC19 plasmid_example_pUC19c
Stack overlapping genes or features on local lanesposition_feature_stack
Place both feature strands on one shared bandposition_plasmid
Place features on opposite sides according to strandposition_strand
Place a quantitative layer in an explicit sequence-local bandposition_track
Prepare named ggchord tables with an explicit audit trailprepare_ggchord_data
Inspect the bundled sequencing-primer catalogueprimer_catalog
Print a cleaned ggchord data resultprint.ggchord_clean
Project protein domains or genomic features through a spliced CDS mapproject_ggchord_features
Project explicitly ungapped protein links to genomic coding segmentsproject_ggchord_links
Six pairwise BLASTp alignments between the example proteinsprotein_ribbon_data_example
Four complete protein sequences for comparisonprotein_seq_data_example
Read BED intervals as ggchord featuresread_bed
Read one or more BLAST tabular output files into ribbon_data formatread_blast
Read one or more FASTA files into seq_data formatread_fasta_lengths
Import local GenBank or GBFF records using an optional mature parserread_genbank
Read one or more GFF3 files into gene_data formatread_gff3
Read PAF mappings as ggchord linksread_paf
Restriction sites for the minimal single-genome fixturerestriction_site_example
Example alignment dataribbon_data_example
Plasmid-map feature presetsscale_feature_fill_plasmid scale_feature_shape_plasmid
Feature shape scalescale_feature_shape_manual
Gene, feature and region fill scalesscale_feature_fill_manual scale_gene_fill_manual scale_region_fill_manual
Scales for point linksscale_link scale_link_alpha_continuous scale_link_alpha_manual scale_link_color_gradientn scale_link_color_manual scale_link_colour_gradientn scale_link_colour_manual scale_link_linetype_manual scale_link_linewidth_continuous scale_link_linewidth_manual
Ribbon alpha, outline and linetype scalesscale_ribbon_alpha_continuous scale_ribbon_alpha_manual scale_ribbon_color_manual scale_ribbon_colour_manual scale_ribbon_linetype_manual
Ribbon fill scalesscale_ribbon_fill_gradientn scale_ribbon_fill_identity scale_ribbon_fill_manual scale_ribbon_fill_stepsn
Sequence colour scalesscale_seq_color_manual scale_seq_colour_manual
Genomic sequence position scalescale_seq_position_continuous
Explicit sequence ring scalescale_seq_ring_manual
Set a track's fill or colour mappingscale_track_colour_gradientn scale_track_colour_manual scale_track_fill_gradientn scale_track_fill_manual
Set a named track's numerical height scalescale_track_value_continuous
Prepare independent windows for a segmented linear displaysegment_ggchord_data
Example sequence dataseq_data_example
Minimal single-genome gene fixturesingle_gene_example
Minimal single-genome sequence fixturesingle_genome_example
Bundle ribbons as a ggchord statstat_ribbon_bundle
Compute local ribbon density as a ggchord statstat_ribbon_density
ggchord themestheme_ggchord theme_ggchord_dark theme_ggchord_minimal theme_ggchord_plasmid theme_ggchord_publication
Validate ggchord input data before plottingvalidate_ggchord_data
Validate explicit genome and contig relationshipsvalidate_ggchord_hierarchy
Preview a ggchord plot at its intended export sizeview_ggchord