Package: ggDNAvis 1.0.1.9002

ggDNAvis: 'ggplot2'-Based Tools for Visualising DNA Sequences and Modifications

Uses 'ggplot2' to visualise either (a) a single DNA/RNA sequence split across multiple lines, (b) multiple DNA/RNA sequences, each occupying a whole line, or (c) base modifications such as DNA methylation called by modified bases models in Dorado or Guppy. Functions starting with visualise_<>() are the main plotting functions, and functions starting with extract_and_sort_<>() are key helper functions for reading files and reformatting data. Source code is available at <https://github.com/ejade42/ggDNAvis>, a full non-expert user guide is available at <https://ejade42.github.io/ggDNAvis/>, and an interactive web-app version of the software is available at <https://ejade42.github.io/ggDNAvis/articles/interactive_app.html>.

Authors:Evelyn Jade [aut, cre, cph]

ggDNAvis_1.0.1.9002.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggDNAvis/json (API)

# Install 'ggDNAvis' in R:

install.packages('ggDNAvis', repos = c('https://ejade42.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ejade42/ggdnavis/issues

Pkgdown/docs site:https://ejade42.github.io

Datasets:

example_many_sequences - Example multiple sequences data
fastq_quality_scores - Vector of the quality scores used by the FASTQ format
sequence_col_palettes - Colour palettes for sequence visualisations
sequence_color_palettes - Colour palettes for sequence visualisations
sequence_colour_palettes - Colour palettes for sequence visualisations

On CRAN:

5.96 score 4 stars 13 scripts 497 downloads 50 exports 36 dependencies

Last updated from:48565d864d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	205
source / vignettes	OK	252
linux-release-x86_64	OK	197
macos-release-arm64	OK	128
macos-oldrel-arm64	OK	122
windows-devel	OK	181
windows-release	OK	151
windows-oldrel	OK	153
wasm-release	OK	120

Exports:bad_arg convert_base_to_number convert_locations_to_MM_vector convert_MM_vector_to_locations convert_modification_to_number_vector convert_sequence_to_numbers convert_sequences_to_matrix create_image_data debug_join_vector_num debug_join_vector_str extract_and_sort_methylation extract_and_sort_sequences extract_methylation_from_dataframe extract_sequences_from_dataframe format_time_diff ggDNAvis_shiny ggDNAvis_shinyapp insert_at_indices merge_fastq_with_metadata merge_methylation_with_metadata monitor monitor_start rasterise_index_annotations rasterise_matrix rasterise_probabilities rasterize_index_annotations rasterize_matrix rasterize_probabilities read_fastq read_modified_fastq resolve_alias resolve_alias_map reverse_complement reverse_locations_if_needed reverse_probabilities_if_needed reverse_quality_if_needed reverse_sequence_if_needed string_to_vector strip_leading_at vector_to_string visualise_many_sequences visualise_methylation visualise_methylation_colour_scale visualise_single_sequence visualize_many_sequences visualize_methylation visualize_methylation_color_scale visualize_single_sequence write_fastq write_modified_fastq

Dependencies:base64enc cli cpp11 dplyr farver generics ggnewscale ggplot2 glue gtable isoband jsonlite labeling lifecycle magrittr pillar pkgconfig png purrr R6 ragg RColorBrewer rlang S7 scales stringi stringr systemfonts textshaping tibble tidyr tidyselect utf8 vctrs viridisLite withr

Interactive App

Rendered frominteractive_app.Rmdusingknitr::rmarkdown

Last update: 2026-01-15
Started: 2026-01-14

Help page	Topics
Emit an error message for an invalid function argument (generic 'ggDNAvis' helper)	bad_arg
Map a single base to the corresponding number (generic 'ggDNAvis' helper)	convert_base_to_number
Convert absolute index locations to MM tag ('write_modified_fastq()' helper)	convert_locations_to_MM_vector
Convert MM tag to absolute index locations (deprecated helper)	convert_MM_vector_to_locations
Convert string-ified modification probabilities and locations to a single vector of probabilities ('visualise_methylation()' helper)	convert_modification_to_number_vector
Map a sequence to a vector of numbers (generic 'ggDNAvis' helper)	convert_sequence_to_numbers
Convert vector of sequences to character matrix (generic 'ggDNAvis' helper)	convert_sequences_to_matrix
Rasterise a vector of sequences into a numerical dataframe for ggplotting (generic 'ggDNAvis' helper)	create_image_data
Print a numeric vector to console ('ggDNAvis' debug helper)	debug_join_vector_num
Print a character/string vector to console ('ggDNAvis' debug helper)	debug_join_vector_str
Example multiple sequences data	example_many_sequences
Extract methylation information from dataframe for visualisation	extract_and_sort_methylation extract_methylation_from_dataframe
Extract, sort, and add spacers between sequences in a dataframe	extract_and_sort_sequences extract_sequences_from_dataframe
Vector of the quality scores used by the FASTQ format	fastq_quality_scores
Format a difference between times (generic 'ggDNAvis' helper)	format_time_diff
'ggDNAvis' aliases	aliases ggDNAvis_aliases
Run the interactive 'ggDNAvis' shinyapp	ggDNAvis_shiny ggDNAvis_shinyapp
Insert blank items at specified indices in a vector ('visualise_many_sequences()' helper)	insert_at_indices
Merge FASTQ data with metadata	merge_fastq_with_metadata
Merge methylation with metadata	merge_methylation_with_metadata
Continue performance monitoring (generic 'ggDNAvis' helper)	monitor
Start performance monitoring (generic 'ggDNAvis' helper)	monitor_start
Process index annotations and rasterise to a x/y/layer dataframe (generic 'ggDNAvis' helper)	rasterise_index_annotations rasterize_index_annotations visualize_index_annotations
Rasterise a matrix to an x/y/layer dataframe (generic 'ggDNAvis' helper)	rasterise_matrix rasterize_matrix
Create dataframe of locations and rendered probabilities ('visualise_methylation()' helper)	rasterise_probabilities rasterize_probabilities
Read sequence and quality information from FASTQ	read_fastq
Read modification information from modified FASTQ	read_modified_fastq
Resolve argument value when aliases are used (generic 'ggDNAvis' helper)	resolve_alias
Process an alias map list (generic 'ggDNAvis' helper)	resolve_alias_map
Reverse complement a DNA/RNA sequence (generic 'ggDNAvis' helper)	reverse_complement
Reverse modification locations if needed ('merge_methylation_with_metadata()' helper)	reverse_locations_if_needed
Reverse modification probabilities if needed ('merge_methylation_with_metadata()' helper)	reverse_probabilities_if_needed
Reverse qualities if needed ('merge_methylation_with_metadata()' helper)	reverse_quality_if_needed
Reverse sequences if needed ('merge_methylation_with_metadata()' helper)	reverse_sequence_if_needed
Colour palettes for sequence visualisations	sequence_color_palettes sequence_colour_palettes sequence_col_palettes
Split a '","'-joined string back to a vector (generic 'ggDNAvis' helper)	string_to_vector
Strip leading '@' from character vector	strip_leading_at
Join a vector into a comma-separated string (generic 'ggDNAvis' helper)	vector_to_string
Visualise many DNA/RNA sequences	visualise_many_sequences visualize_many_sequences
Visualise methylation probabilities for many DNA sequences	visualise_methylation visualize_methylation
Visualise methylation colour scalebar	visualise_methylation_colour_scale visualize_methylation_color_scale
Visualise a single DNA/RNA sequence	visualise_single_sequence visualize_single_sequence
Write sequence and quality information to FASTQ	write_fastq
Write modification information stored in dataframe back to modified FASTQ	write_modified_fastq

Package: ggDNAvis 1.0.1.9002

ggDNAvis: 'ggplot2'-Based Tools for Visualising DNA Sequences and Modifications

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