Package index • ggDNAvis

DNA visualisation

Alias information

Information on how function and argument aliases are implemented in ggDNAvis

ggDNAvis_aliases aliases: ggDNAvis aliases

Main visualisation functions

Main functions for visualising DNA/RNA/methylation information

ggDNAvis_shinyapp(): Run the interactive ggDNAvis shinyapp
visualise_single_sequence(): Visualise a single DNA/RNA sequence
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

Key data processing functions

Frequently used functions for importing and processing

read_fastq(): Read sequence and quality information from FASTQ
read_modified_fastq(): Read modification information from modified FASTQ
write_fastq(): Write sequence and quality information to FASTQ
write_modified_fastq(): Write modification information stored in dataframe back to modified FASTQ
merge_fastq_with_metadata(): Merge FASTQ data with metadata
merge_methylation_with_metadata(): Merge methylation with metadata
extract_and_sort_sequences(): Extract, sort, and add spacers between sequences in a dataframe
extract_and_sort_methylation(): Extract methylation information from dataframe for visualisation

Included data

Data included in ggDNAvis

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

Basic helpers

Small, widely used helper functions

string_to_vector(): Split a ","-joined string back to a vector (generic ggDNAvis helper)
vector_to_string(): Join a vector into a comma-separated string (generic ggDNAvis helper)
reverse_complement(): Reverse complement a DNA/RNA sequence (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)
bad_arg(): Emit an error message for an invalid function argument (generic ggDNAvis helper)
resolve_alias(): Resolve argument value when aliases are used (generic ggDNAvis helper)

Advanced helpers

Helper functions that are mostly called by other functions; users shouldn’t need these for normal use cases (but they could be helpful if you need to do similar data processing steps for other workflows, so they are available if needed)

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_sequence_to_numbers(): Map a sequence to a vector of numbers (generic ggDNAvis helper)
convert_sequences_to_matrix(): Convert vector of sequences to character matrix (generic ggDNAvis helper)
create_image_data(): Rasterise a vector of sequences into a numerical dataframe for ggplotting (generic ggDNAvis helper)
insert_at_indices(): Insert blank items at specified indices in a vector (visualise_many_sequences() 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)
reverse_sequence_if_needed(): Reverse sequences if needed (merge_methylation_with_metadata() helper)
reverse_quality_if_needed(): Reverse qualities if needed (merge_methylation_with_metadata() 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)