'ggplot2'-Based Tools for Visualising DNA Sequences and
Modifications
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Documentation for package ‘ggDNAvis’ version 1.0.0
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 |