A Grammar of Graphics for Comparative Genomics

Documentation for package ‘gggenomes’ version 1.0.0

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-- A --

add_class	Modify object class attriutes
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

-- 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_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 attriutes
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 attriutes
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

-- V --

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