GeomFeatText            Geom for feature text
add_feats               Add different types of tracks
add_seqs                Add seqs
align                   Align genomes relative to target genes, feats,
                        seqs, etc.
check_strand            Check strand
combine_strands         Combine strands
def_formats             Defined file formats and extensions
def_names               Default column names and types for defined
                        formats
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
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
ex                      Get path to gggenomes example files
feats                   Use tracks inside and outside geom_* calls
flip                    Flip bins and sequences
flip_strand             Flip strand
focus                   Show features and regions of interest
geom_bin_label          Draw bin labels
geom_coverage           Draw wiggle ribbons or lines
geom_feat               Draw feats
geom_feat_text          Add text to genes, features, etc.
geom_gene               Draw gene models
geom_gene_label         Draw feat/link labels
geom_link               Draw links between genomes
geom_seq                draw seqs
geom_seq_break          Decorate truncated sequences
geom_seq_label          Draw seq labels
geom_variant            Draw place of mutation
get_seqs                Get/set the seqs track
gggenomes               Plot genomes, features and synteny maps
if_reverse              Vectorised if_else based on strandedness
in_range                Do numeric values fall into specified ranges?
introduce               Introduce non-existing columns
is_reverse              Check whether strand is reverse
layout                  Re-layout a genome layout
layout_seqs             Layout sequences
pick                    Pick bins and seqs by name or position
position_strand         Stack features
position_variant        Plot types of mutations with different offsets
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 sequence index
read_tracks             Read files in various standard formats (FASTA,
                        GFF3, GBK, BED, BLAST, ...) into track tables
read_vcf                Read a VCF file
require_vars            Require variables in an object
scale_color_variant     Default colors and shapes for mutation types.
scale_x_bp              X-scale for genomic data
set_class               Modify object class attributes
shift                   Shift bins left/right
strand_chr              Convert strand to character
strand_int              Convert strand to integer
strand_lgl              Convert strand to logical
swap_if                 Swap values of two columns based on a condition
swap_query              Swap query and subject in blast-like feature
                        tables
theme_gggenomes_clean   gggenomes default theme
track_ids               Named vector of track ids and types
track_info              Basic info on tracks in a gggenomes object
unnest_exons            Unnest exons
vars_track              Tidyselect track variables
width                   The width of a range
write_gff3              Write a gff3 file from a tidy table
