Function reference • gggenomes

Set up a plot Construct a plot combining multiple tracks
`gggenomes()`	Plot genomes, features and synteny maps
Handle tracks
`track_info()`	Basic info on tracks in a gggenomes object
`add_seqs()`	Add seqs
`add_feats()` `add_links()` `add_subfeats()` `add_sublinks()` `add_clusters()`	Add different types of tracks
`set_class()` `add_class()` `strip_class()`	Modify object class attriutes
`feats()` `feats0()` `genes()` `links()` `seqs()` `bins()` `track()` `pull_feats()` `pull_genes()` `pull_links()` `pull_seqs()` `pull_bins()` `pull_track()`	Use tracks inside and outside `geom_*` calls
Draw geoms & positions
`geom_seq()`	draw seqs
`geom_gene()`	Draw gene models
`geom_feat()`	Draw feats
`geom_link()` `geom_link_line()`	Draw links between genomes
`geom_coverage()` `geom_wiggle()`	Draw wiggle ribbons or lines
`geom_feat_text()` `geom_feat_tag()` `geom_feat_note()` `geom_gene_text()` `geom_gene_tag()` `geom_gene_note()`	Add text to genes, features, etc.
`geom_bin_label()`	Draw bin labels
`geom_gene_label()` `geom_feat_label()` `geom_link_label()`	Draw feat/link labels
`geom_seq_break()`	Decorate truncated sequences
`geom_seq_label()`	Draw seq labels
`geom_variant()`	Draw place of mutation
`position_strand()` `position_pile()` `position_strandpile()` `position_sixframe()`	Stack features
`position_variant()`	Plot types of mutations with different offsets
`scale_x_bp()` `label_bp()`	X-scale for genomic data
`scale_color_variant()` `scale_shape_variant()`	Default colors and shapes for mutation types.
`theme_gggenomes_clean()`	gggenomes default theme
Manipulate plot & data
`pick()` `pick_seqs()` `pick_seqs_within()` `pick_by_tree()`	Pick bins and seqs by name or position
`flip()` `flip_seqs()` `sync()`	Flip bins and sequences
`shift()`	Shift bins left/right
`focus()` `locate()`	Show features and regions of interest
Read data Read common bioinformatics file types
`read_feats()` `read_subfeats()` `read_links()` `read_sublinks()` `read_seqs()`	Read files in various standard formats (FASTA, GFF3, GBK, BED, BLAST, ...) into track tables
`read_alitv()`	Read AliTV .json file
`read_bed()`	Read a BED file
`read_blast()`	Read BLAST tab-separated output
`read_context()`	Read files in different contexts
`read_gbk()`	Read genbank files
`read_gff3()`	Read features from GFF3 (and with some limitations GFF2/GTF) files
`read_paf()`	Read a .paf file (minimap/minimap2).
`read_seq_len()` `read_fai()`	Read sequence index
`read_vcf()`	Read a VCF file
`synteny_to_link()`	Format synteny-class into wide tibble This is for use with gggenomes
`swap_query()`	Swap query and subject in blast-like feature tables
`ex()`	Get path to gggenomes example files
`def_formats()`	Defined file formats and extensions
`def_names()` `def_types()`	Default column names and types for defined formats
`write_gff3()`	Write a gff3 file from a tidy table
Under the hood Functions that power gggenomes under the hood. Useful for developers and power-users.
`layout()`	Re-layout a genome layout
`layout_genomes()`	Layout genomes
`layout_seqs()`	Layout sequences
`get_seqs()` `set_seqs()`	Get/set the seqs track
`track_ids()`	Named vector of track ids and types
`track_info()`	Basic info on tracks in a gggenomes object
`track_nrows()`	Number of rows of all tracks tables
`track_type()`	Track type by track id
`track_types()`	All types of all tracks
`require_vars()`	Require variables in an object
`vars_track()`	Tidyselect track variables
`swap_if()`	Swap values of two columns based on a condition
`split_by()`	Split by key preserving order
`in_range()`	Do numeric values fall into specified ranges?
`width()` `width0()`	The width of a range
`introduce()`	Introduce non-existing columns
`file_label()`	Add a unique name to files
`qw()` `qc()`	Create a vector from unquoted words.
`GeomFeatText`	Geom for feature text
`check_strand()`	Check strand
`combine_strands()`	Combine strands
`drop_feat_layout()`	Drop feature layout
`drop_layout()`	Drop a genome layout
`drop_link_layout()`	Drop a link layout
`drop_seq_layout()`	Drop a seq layout
`flip_strand()`	Flip strand
`if_reverse()`	Vectorised if_else based on strandedness
`is_reverse()`	Check whether strand is reverse
`strand_chr()`	Convert strand to character
`strand_int()`	Convert strand to integer
`strand_lgl()`	Convert strand to logical
`unnest_exons()`	Unnest exons
Data sets
`emale_ava`	All-versus-all whole genome alignments of 6 EMALE genomes
`emale_cogs`	Clusters of orthologs of 6 EMALE proteomes
`emale_gc`	Relative GC-content along 6 EMALE genomes
`emale_genes`	Gene annotations if 6 EMALE genomes (endogenous virophages)
`emale_ngaros`	Integrated Ngaro retrotransposons of 6 EMALE genomes
`emale_prot_ava`	All-versus-all alignments 6 EMALE proteomes
`emale_seqs`	Sequence index of 6 EMALE genomes (endogenous virophages)
`emale_tirs`	Terminal inverted repeats of 6 EMALE genomes

Reference

Set up a plot

Handle tracks

Draw geoms & positions

Manipulate plot & data

Read data

Under the hood

Data sets