Package index • 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

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

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

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