# Multi-Sequence Alignment Chord Diagram Visualization Tool

## Documentation for package ‘ggchord’ version 0.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

+.ggchord | Combine a ggchord plot with ggplot2 objects
as.data.frame.ggchord_validation | Coerce a validation result to a flat data.frame
clean_ggchord_data | Clean ggchord input data with explicit, report-driven policies
coord_chord | Chord diagram coordinate system
deduplicate_ggchord_ribbons | Deduplicate alignment ribbons
filter_ggchord_ribbons | Filter alignment ribbons before plotting
gene_data_example | Example gene annotation data
geom_axis | Add an axis layer
geom_feature | Draw generic genomic features
geom_gene | Add a gene arrow layer
geom_gene_label | Add a gene label layer
geom_gene_label_repel | Add a repelled gene label layer (ggrepel-style)
geom_ribbon | Add an alignment ribbon layer
geom_ribbon_highlight | Highlight selected alignment ribbons
geom_seq | Add a sequence arc layer
geom_seq_label | Add a sequence label layer
geom_seq_region | Highlight regions along sequence arcs
get_chord_layout | Get the chord layout from the package environment
ggchord | ggchord: layered multi-sequence alignment chord diagrams for ggplot2
ggplotly.ggchord | Convert a ggchord plot to a plotly object
merge_ggchord_ribbons | Merge adjacent or overlapping alignment blocks of the same sequence pair
print.ggchord_clean | Print a cleaned ggchord data result
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_gff3 | Read one or more GFF3 files into gene_data format
ribbon_data_example | Example alignment data
seq_data_example | Example sequence data
validate_ggchord_data | Validate ggchord input data before plotting