Package index • ggDNAvis

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DNA visualisation

Main visualisation functions

Main functions for visualising DNA/RNA/methylation information

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_methylation_from_dataframe(): 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)

Advanced helpers

Helper functions that are mostly called by other functions; users shouldn’t need these for normal use cases

convert_base_to_number(): Map a single base to the corresponding number (generic ggDNAvis helper)

convert_input_seq_to_sequence_list(): Split a single input sequence into a vector of "lines" for visualisation (visualise_single_sequence() 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 (read_modified_fastq() 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_annotations(): Convert a vector of sequences to a dataframe for plotting sequence contents and index annotations (visualise_single_sequence() helper)

create_image_data(): Rasterise a vector of sequences into a numerical dataframe for ggplotting (generic ggDNAvis 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)