Package: gggenomes 1.0.1

gggenomes: A Grammar of Graphics for Comparative Genomics

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.

Authors:Thomas Hackl [aut, cre], Markus J. Ankenbrand [aut], Bart van Adrichem [aut], Kristina Haslinger [ctb, sad]

gggenomes_1.0.1.tar.gz
gggenomes_1.0.1.zip(r-4.5)gggenomes_1.0.1.zip(r-4.4)gggenomes_1.0.1.zip(r-4.3)
gggenomes_1.0.1.tgz(r-4.4-any)gggenomes_1.0.1.tgz(r-4.3-any)
gggenomes_1.0.1.tar.gz(r-4.5-noble)gggenomes_1.0.1.tar.gz(r-4.4-noble)
gggenomes_1.0.1.tgz(r-4.4-emscripten)gggenomes_1.0.1.tgz(r-4.3-emscripten)
gggenomes.pdf |gggenomes.html✨
gggenomes/json (API)

# Install 'gggenomes' in R:
install.packages('gggenomes', repos = c('https://thackl.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/thackl/gggenomes/issues

Datasets:
  • 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
  • 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
  • emale_tirs - Terminal inverted repeats of 6 EMALE genomes

On CRAN:

biological-datacomparative-genomicsgenomics-visualizationggplot-extensionggplot2

9.29 score 593 stars 109 scripts 348 downloads 127 exports 49 dependencies

Last updated 3 months agofrom:976bb83197. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:%<>%%>%add_classadd_clustersadd_featsadd_linksadd_seqsadd_subfeatsadd_sublinksas_featsas_linksas_seqsas_subfeatsas_sublinksbinscheck_strandcombine_strandsdef_formatsdef_namesdef_typesdrop_feat_layoutdrop_layoutdrop_link_layoutdrop_seq_layoutexfeatsfeats0flipflip_seqsflip_strandfocusgenesgeom_bin_labelgeom_coveragegeom_featgeom_feat_labelgeom_feat_notegeom_feat_taggeom_feat_textgeom_genegeom_gene_labelgeom_gene_notegeom_gene_taggeom_gene_textgeom_linkgeom_link_labelgeom_link_linegeom_seqgeom_seq_breakgeom_seq_labelgeom_variantgeom_wiggleGeomFeatTextget_seqsgggenomeshas_varsif_reversein_rangeintroduceis_reverselabel_bplayoutlayout_genomeslayout_seqslinkslocatepickpick_by_treepick_seqspick_seqs_withinposition_pileposition_sixframeposition_strandposition_strandpileposition_variantPositionPilePositionSixframePositionStrandPositionStrandpilepull_binspull_featspull_genespull_linkspull_seqspull_trackqcqwread_alitvread_bedread_blastread_contextread_fairead_featsread_gbkread_gff3read_linksread_pafread_seq_lenread_seqsread_subfeatsread_sublinksread_vcfrequire_varsscale_color_variantscale_shape_variantscale_x_bpseqsset_classset_seqsshiftsplit_bystrand_chrstrand_intstrand_lglstrip_classswap_ifswap_querysynctheme_gggenomes_cleantracktrack_idstrack_infounnest_exonsvars_trackwidthwidth0write_gff3

Dependencies:bitbit64clicliprcolorspacecpp11crayondplyrellipsisfansifarvergenericsggplot2gluegtablehmsisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangscalessnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr

gggenomes - a multi-track ggplot2 extension for comparative genomics

Thomas Hackl

Rendered fromgggenomes.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-08-30
Started: 2021-06-01

From a few sequences to a complex map in minutes (old version)

Thomas Hackl

Rendered fromemales.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-03-05
Started: 2020-05-12

Advanced flip examples

Thomas Hackl

Rendered fromflip.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-06-28
Started: 2024-06-28

Readme and manuals

Help Manual

Help pageTopics
Add different types of tracksadd_clusters add_feats add_links add_subfeats add_sublinks add_tracks
Add seqsadd_seqs
Check strandcheck_strand
Combine strandscombine_strands
Defined file formats and extensionsdef_formats
Default column names and types for defined formatsdef_names def_types
Drop feature layoutdrop_feat_layout
Drop a genome layoutdrop_layout
Drop a link layoutdrop_link_layout
Drop a seq layoutdrop_seq_layout
All-versus-all whole genome alignments of 6 EMALE genomesemale_ava
Clusters of orthologs of 6 EMALE proteomesemale_cogs
Relative GC-content along 6 EMALE genomesemale_gc
Gene annotations if 6 EMALE genomes (endogenous virophages)emale_genes
Integrated Ngaro retrotransposons of 6 EMALE genomesemale_ngaros
All-versus-all alignments 6 EMALE proteomesemale_prot_ava
Sequence index of 6 EMALE genomes (endogenous virophages)emale_seqs
Terminal inverted repeats of 6 EMALE genomesemale_tirs
Get path to gggenomes example filesex
Use tracks inside and outside geom_* callsbins feats feats0 genes links pull_bins pull_bins.gggenomes_layout pull_feats pull_genes pull_links pull_seqs pull_track seqs track
Flip bins and sequencesflip flip_seqs sync
Flip strandflip_strand
Show features and regions of interestfocus locate
Draw bin labelsgeom_bin_label
Draw wiggle ribbons or linesgeom_coverage geom_wiggle
Draw featsgeom_feat
Add text to genes, features, etc.geom_feat_note geom_feat_tag geom_feat_text geom_gene_note geom_gene_tag geom_gene_text
Draw gene modelsgeom_gene
Draw feat/link labelsgeom_feat_label geom_gene_label geom_link_label
Draw links between genomesgeom_link geom_link_line
draw seqsgeom_seq
Decorate truncated sequencesgeom_seq_break
Draw seq labelsgeom_seq_label
Draw place of mutationgeom_variant
Geom for feature textGeomFeatText
Get/set the seqs trackget_seqs set_seqs
Plot genomes, features and synteny mapsgggenomes
Vectorised if_else based on strandednessif_reverse
Do numeric values fall into specified ranges?in_range
Introduce non-existing columnsintroduce
Check whether strand is reverseis_reverse
Re-layout a genome layoutlayout
Layout sequenceslayout_seqs
Pick bins and seqs by name or positionpick pick_by_tree pick_seqs pick_seqs_within
Stack featuresPositionPile PositionSixframe PositionStrand PositionStrandpile position_pile position_sixframe position_strand position_strandpile
Plot types of mutations with different offsetsposition_variant
Read AliTV .json fileread_alitv
Read a BED fileread_bed
Read BLAST tab-separated outputread_blast
Read files in different contextsread_context
Read genbank filesread_gbk
Read features from GFF3 (and with some limitations GFF2/GTF) filesread_gff3
Read a .paf file (minimap/minimap2).read_paf
Read sequence indexread_fai read_seq_len
Read files in various standard formats (FASTA, GFF3, GBK, BED, BLAST, ...) into track tablesread_feats read_links read_seqs read_subfeats read_sublinks read_tracks
Read a VCF fileread_vcf
Require variables in an objectrequire_vars
Default colors and shapes for mutation types.scale_color_variant scale_shape_variant
X-scale for genomic datalabel_bp scale_x_bp
Modify object class attriutesadd_class set_class strip_class
Shift bins left/rightshift
Convert strand to characterstrand_chr
Convert strand to integerstrand_int
Convert strand to logicalstrand_lgl
Swap values of two columns based on a conditionswap_if
Swap query and subject in blast-like feature tablesswap_query
gggenomes default themetheme_gggenomes_clean
Named vector of track ids and typestrack_ids
Basic info on tracks in a gggenomes objecttrack_info
Unnest exonsunnest_exons
Tidyselect track variablesvars_track
The width of a rangewidth width0
Write a gff3 file from a tidy tablewrite_gff3