Man pages for thackl/gggenomes
A Grammar of Graphics for Comparative Genomics
| add_seqs | Add seqs |
| add_tracks | Add different types of tracks |
| anchor | The virtual x-start of the full length seq in the plot |
| 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 |
| as_tracks | Convert a list of tibbles into tracks with magic |
| check_strand | Check strand |
| combine_strands | Combine strands |
| comma | Collapse a string with commas |
| 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 |
| file_label | Add a unique name to 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_seqlen | Helper to extract seqlengths from DECIPHER::FindSyntney... |
| 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_feats | Layout feats |
| layout_genomes | Layout genomes |
| layout_links | Layout tbl_link |
| layout_seqs | Layout sequences |
| match_arg | match.arg defaulting to all choices |
| 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 |
| synteny_to_link | Format synteny-class into wide tibble This is for use with... |
| 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 |
| track_nrows | Number of rows of all tracks tables |
| track_type | Track type by track id |
| track_types | All types of all tracks |
| unnest_exons | Unnest exons |
| vars_track | Tidyselect track variables |
| vars_track_error | Error messages for vars_track |
| width | The width of a range |
| write_gff3 | Write a gff3 file from a tidy table |
| x | Project feat coordinates into layout space |
