A Grammar of Graphics for Comparative Genomics
Add different types of tracks
Introduce non-existing columns
Check whether strand is reverse
Layout genomes
Layout sequences
Re-layout a genome layout
Pick bins and seqs by name or position
Shift bins left/right
Split by key preserving order
Convert strand to character
Convert strand to integer
Convert strand to logical
Swap values of two columns based on a condition
Swap query and subject in blast-like feature tables
gggenomes default theme
Named vector of track ids and types
Basic info on tracks in a gggenomes object
Unnest exons
Tidyselect track variables
The width of a range
Write a gff3 file from a tidy table
Do numeric values fall into specified ranges?
Add seqs
Check if variables exist in object
Align genomes relative to target genes, feats, seqs, etc.
Compute a layout for feat data
Compute a layout for link data
Compute a layout for sequence data
Compute a layout for subfeat data
Vectorised if_else based on strandedness
Compute a layout for links linking feats
Check strand
Combine strands
Defined file formats and extensions
Default column names and types for defined formats
ggplot2::facet_null checks data with empty(df) using dim. This c...
Drop feature layout
Drop a genome layout
Drop a link layout
Drop a seq layout
Get path to gggenomes example files
Flip strand
Flip bins and sequences
Show features and regions of interest
Draw bin labels
Add text to genes, features, etc.
Draw feats
Draw feat/link labels
Draw gene models
Draw links between genomes
Decorate truncated sequences
Draw seq labels
draw seqs
Draw place of mutation
Draw wiggle ribbons or lines
Geom for feature text
Get/set the seqs track
Plot genomes, features and synteny maps
Stack features
Plot types of mutations with different offsets
Use tracks inside and outside geom_* calls
Create a vector from unquoted words.
Read AliTV .json file
Read a BED file
Read BLAST tab-separated output
Read files in different contexts
Read genbank files
Read features from GFF3 (and with some limitations GFF2/GTF) files
Read a .paf file (minimap/minimap2).
Read sequence index
Read files in various standard formats (FASTA, GFF3, GBK, BED, BLAST, ...
Read a VCF file
Objects exported from other packages
Require variables in an object
Default colors and shapes for mutation types.
X-scale for genomic data
Modify object class attributes
An extension of 'ggplot2' for creating complex genomic maps. It builds on the power of 'ggplot2' and 'tidyverse' adding new 'ggplot2'-style geoms & positions and 'dplyr'-style verbs to manipulate the underlying data. It implements a layout concept inspired by 'ggraph' and introduces tracks to bring tidiness to the mess that is genomics data.
Useful links