'ggplot2'-Based Tools for Visualising DNA Sequences and Modifications
Print a numeric vector to console (ggDNAvis debug helper)
Map a single base to the corresponding number (generic ggDNAvis help...
Split a single input sequence into a vector of "lines" for visualisati...
Convert absolute index locations to MM tag (write_modified_fastq() h...
Convert MM tag to absolute index locations (read_modified_fastq() he...
Convert string-ified modification probabilities and locations to a sin...
Map a sequence to a vector of numbers (generic ggDNAvis helper)
Convert a vector of sequences to a dataframe for plotting sequence con...
Rasterise a vector of sequences into a numerical dataframe for ggplott...
Print a character/string vector to console (ggDNAvis debug helper)
Extract, sort, and add spacers between sequences in a dataframe
Extract methylation information from dataframe for visualisation
ggDNAvis: 'ggplot2'-Based Tools for Visualising DNA Sequences and Modi...
Merge FASTQ data with metadata
Merge methylation with metadata
Rasterise a matrix to an x/y/layer dataframe (generic ggDNAvis helpe...
Read sequence and quality information from FASTQ
Read modification information from modified FASTQ
Reverse complement a DNA/RNA sequence (generic ggDNAvis helper)
Reverse modification locations if needed (`merge_methylation_with_meta...
Reverse modification probabilities if needed (`merge_methylation_with_...
Reverse qualities if needed (merge_methylation_with_metadata() helpe...
Reverse sequences if needed (merge_methylation_with_metadata() helpe...
Split a ","-joined string back to a vector (generic ggDNAvis helpe...
Join a vector into a comma-separated string (generic ggDNAvis helper...
Visualise many DNA/RNA sequences
Visualise methylation colour scalebar
Visualise methylation probabilities for many DNA sequences
Visualise a single DNA/RNA sequence
Write sequence and quality information to FASTQ
Write modification information stored in dataframe back to modified FA...
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_<something>() are the main plotting functions, and functions starting with extract_<something>() are key helper functions for reading files and reformatting data. Source code is available at <https://github.com/ejade42/ggDNAvis> and a full non-expert user guide is available at <https://ejade42.github.io/ggDNAvis/>.
Useful links