# 'ggplot2'-Based Tools for Visualising DNA Sequences and Modifications

## Documentation for package ‘ggDNAvis’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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