Package index

Plot construction

Build and inspect ggchord plots.

ggchord()

ggchord: layered multi-sequence alignment chord diagrams for ggplot2

coord_chord()

Chord diagram coordinate system

get_chord_layout()

Get the chord layout from the package environment

`+`(<ggchord>)

Combine a ggchord plot with ggplot2 objects

Methods and datasets

S3 methods and example data shipped with ggchord.

as.data.frame(<ggchord_validation>)

Coerce a validation result to a flat data.frame

print(<ggchord_clean>)

Print a cleaned ggchord data result

seq_data_example

Example sequence data

ribbon_data_example

Example alignment data

gene_data_example

Example gene annotation data

Layers

Stack geometry, annotation, axis and label layers.

geom_seq()

Add a sequence arc layer

geom_ribbon()

Add an alignment ribbon layer

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_axis()

Add an axis layer

geom_seq_label()

Add a sequence label layer

geom_seq_region()

Highlight regions along sequence arcs

geom_ribbon_highlight()

Highlight selected alignment ribbons

geom_feature()

Draw generic genomic features

Scales

Control sequence, ribbon, feature and genomic-position aesthetics.

scale_seq_colour_manual() scale_seq_color_manual()

Sequence colour scales

scale_ribbon_fill_stepsn() scale_ribbon_fill_gradientn() scale_ribbon_fill_manual() scale_ribbon_fill_identity()

Ribbon fill scales

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_gene_fill_manual() scale_feature_fill_manual() scale_region_fill_manual()

Gene, feature and region fill scales

scale_feature_shape_manual()

Feature shape scale

scale_seq_position_continuous()

Genomic sequence position scale

Themes and guides

Apply publication-ready themes and legend defaults.

theme_ggchord() theme_ggchord_minimal() theme_ggchord_dark() theme_ggchord_publication()

ggchord themes

guide_ggchord_legend() guide_ggchord_colourbar()

Guides for ggchord role aesthetics

Data import

Read FASTA, BLAST and GFF3 files in R.

read_fasta_lengths()

Read one or more FASTA files into seq_data format

read_blast()

Read one or more BLAST tabular output files into ribbon_data format

read_gff3()

Read one or more GFF3 files into gene_data format

Validation and cleaning

Check and repair ggchord input tables before plotting.

validate_ggchord_data()

Validate ggchord input data before plotting

clean_ggchord_data()

Clean ggchord input data with explicit, report-driven policies

Ribbon preparation

Filter, deduplicate and merge alignment blocks.

filter_ggchord_ribbons()

Filter alignment ribbons before plotting

deduplicate_ggchord_ribbons()

Deduplicate alignment ribbons

merge_ggchord_ribbons()

Merge adjacent or overlapping alignment blocks of the same sequence pair