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_feats() add_links() add_subfeats() add_sublinks() add_clusters()

Add different types of tracks

feats() 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()

Draw links

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()

draw feat labels

geom_link_label()

draw link labels

geom_seq_label()

draw feat labels

position_strand() position_pile() position_strandpile() position_sixframe()

Stack features

scale_x_bp() label_bp()

X-scale for genomic data

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() flip_by_links()

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

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

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

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_prot_uniref50

Alignments of 6 EMALE proteomes against Uniref50

emale_seqs

Sequence index of 6 EMALE genomes (endogenous virophages)

emale_tirs

Terminal inverted repeats of 6 EMALE genomes