add_seqs | Add seqs |
add_tracks | Add different types of tracks |
as_feats | Compute a layout for feat data |
as_links | Compute a layout for link data |
as_seqs | Compute a layout for sequence data |
as_subfeats | Compute a layout for subfeat data |
as_sublinks | Compute a layout for links linking feats |
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 |
dim.gggenomes_layout | 'ggplot2::facet_null' checks data with 'empty(df)' using... |
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 |
flip | Flip bins and sequences |
flip_strand | Flip strand |
focus | Show features and regions of interest |
geom_bin_label | Draw bin labels |
geom_feat | Draw feats |
geom_feat_text | Add text to genes, features, etc. |
GeomFeatText | Geom for feature text |
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 |
geom_wiggle | Draw wiggle ribbons or lines |
get_seqs | Get/set the seqs track |
gggenomes | Plot genomes, features and synteny maps |
ggplot.gggenomes_layout | ggplot.default tries to 'fortify(data)' and we don't want... |
has_vars | Check if variables exist in object |
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_genomes | Layout genomes |
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 |
pull_track | Use tracks inside and outside geom_* calls |
qw | Create a vector from unquoted words. |
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)... |
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,... |
read_vcf | Read a VCF file |
reexports | Objects exported from other packages |
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 attriutes |
shift | Shift bins left/right |
split_by | Split by key preserving order |
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 |
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