# A Grammar of Graphics for Comparative Genomics

## Documentation for package ‘gggenomes’ version 1.1.2

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

## Help Pages

A B C D E F G I L P R S T U V W

## -- A --

add_class | Modify object class attributes
add_clusters | Add different types of tracks
add_feats | Add different types of tracks
add_links | Add different types of tracks
add_seqs | Add seqs
add_subfeats | Add different types of tracks
add_sublinks | Add different types of tracks
add_tracks | Add different types of tracks
align | Align genomes relative to target genes, feats, seqs, etc.

## -- B --

bins | Use tracks inside and outside geom_* calls

## -- C --

check_strand | Check strand
combine_strands | Combine strands

## -- D --

def_formats | Defined file formats and extensions
def_names | Default column names and types for defined formats
def_types | 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

## -- E --

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

## -- F --

feats | Use tracks inside and outside geom_* calls
feats0 | Use tracks inside and outside geom_* calls
flip | Flip bins and sequences
flip_seqs | Flip bins and sequences
flip_strand | Flip strand
focus | Show features and regions of interest

## -- G --

genes | Use tracks inside and outside geom_* calls
GeomFeatText | Geom for feature text
geom_bin_label | Draw bin labels
geom_coverage | Draw wiggle ribbons or lines
geom_feat | Draw feats
geom_feat_label | Draw feat/link labels
geom_feat_note | Add text to genes, features, etc.
geom_feat_tag | Add text to genes, features, etc.
geom_feat_text | Add text to genes, features, etc.
geom_gene | Draw gene models
geom_gene_label | Draw feat/link labels
geom_gene_note | Add text to genes, features, etc.
geom_gene_tag | Add text to genes, features, etc.
geom_gene_text | Add text to genes, features, etc.
geom_link | Draw links between genomes
geom_link_curved | Draw links between genomes
geom_link_label | Draw feat/link labels
geom_link_line | 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
geom_wiggle | Draw wiggle ribbons or lines
get_seqs | Get/set the seqs track
gggenomes | Plot genomes, features and synteny maps

## -- I --

if_reverse | Vectorised if_else based on strandedness
introduce | Introduce non-existing columns
in_range | Do numeric values fall into specified ranges?
is_reverse | Check whether strand is reverse

## -- L --

label_bp | X-scale for genomic data
layout | Re-layout a genome layout
layout_seqs | Layout sequences
links | Use tracks inside and outside geom_* calls
locate | Show features and regions of interest

## -- P --

pick | Pick bins and seqs by name or position
pick_by_tree | Pick bins and seqs by name or position
pick_seqs | Pick bins and seqs by name or position
pick_seqs_within | Pick bins and seqs by name or position
PositionPile | Stack features
PositionSixframe | Stack features
PositionStrand | Stack features
PositionStrandpile | Stack features
position_pile | Stack features
position_sixframe | Stack features
position_strand | Stack features
position_strandpile | Stack features
position_variant | Plot types of mutations with different offsets
pull_bins | Use tracks inside and outside geom_* calls
pull_bins.gggenomes_layout | Use tracks inside and outside geom_* calls
pull_feats | Use tracks inside and outside geom_* calls
pull_genes | Use tracks inside and outside geom_* calls
pull_links | Use tracks inside and outside geom_* calls
pull_seqs | Use tracks inside and outside geom_* calls
pull_track | Use tracks inside and outside geom_* calls

## -- R --

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_fai | Read sequence index
read_feats | Read files in various standard formats (FASTA, GFF3, GBK, BED, BLAST, ...) into track tables
read_gbk | Read genbank files
read_gff3 | Read features from GFF3 (and with some limitations GFF2/GTF) files
read_links | Read files in various standard formats (FASTA, GFF3, GBK, BED, BLAST, ...) into track tables
read_paf | Read a .paf file (minimap/minimap2).
read_seqs | Read files in various standard formats (FASTA, GFF3, GBK, BED, BLAST, ...) into track tables
read_seq_len | Read sequence index
read_subfeats | Read files in various standard formats (FASTA, GFF3, GBK, BED, BLAST, ...) into track tables
read_sublinks | Read files in various standard formats (FASTA, GFF3, GBK, BED, BLAST, ...) into track tables
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

## -- S --

scale_color_variant | Default colors and shapes for mutation types.
scale_shape_variant | Default colors and shapes for mutation types.
scale_x_bp | X-scale for genomic data
seqs | Use tracks inside and outside geom_* calls
set_class | Modify object class attributes
set_seqs | Get/set the seqs track
shift | Shift bins left/right
strand_chr | Convert strand to character
strand_int | Convert strand to integer
strand_lgl | Convert strand to logical
strip_class | Modify object class attributes
swap_if | Swap values of two columns based on a condition
swap_query | Swap query and subject in blast-like feature tables
sync | Flip bins and sequences

## -- T --

theme_gggenomes_clean | gggenomes default theme
track | Use tracks inside and outside geom_* calls
track_ids | Named vector of track ids and types
track_info | Basic info on tracks in a gggenomes object

## -- U --

unnest_exons | Unnest exons

## -- V --

vars_track | Tidyselect track variables

## -- W --

width | The width of a range
width0 | The width of a range
write_gff3 | Write a gff3 file from a tidy table