ggDNAvis 1.0.0

This major release has enormous changes to pretty much every aspect of ggDNAvis. Expect code to break, but also for performance and features to be enhanced across the board.

New features:

• Interactive web-app now available

  • Can be found on ‘Interactive App’ tab of documentation website

  • Can be launched locally via ggDNAvis_shinyapp().

• Aliases: American spellings should now be available for all major function and argument names.

  • Every instance of visualise should now also work with visualize e.g. visualize_single_sequence().

  • Every instance of colour should now also work with color and col e.g. sequence_text_color or background_col.

  • There is a minor exception in that visualise_methylation_colour_scale() accepts visualize_methylation_color_scale() but does not accept col in the function name (and does not accept mixing visualise with color or visualize with colour).

  • Some aliases are set up for common typos, especially regarding pluralisation. In particular, index_annotations_above also accepts index_annotation_above, and index_annotation_full_line accepts any combination of annotation and line being plural or single.

  • If any aliases which ought to work don’t, please raise an issue at https://github.com/ejade42/ggDNAvis/issues and they can be easily added.

• visualise_many_sequences() and visualise_methylation() now have index annotations!

  • Arguments controlling size, colour, position, and frequency are the same as for visualise_single_sequence().

  • index_annotation_lines controls which lines (counting down from the top) have annotations.

  • index_annotation_full_line controls whether annotations go to the end of each annotated sequence, or all the way to the end of the image.

  • Unlike visualise_single_sequence(), index annotations in visualise_many_sequences() and visualise_methylation() reset each line as each line is a different sequence.

• Index annotations can now be forced to always occur at the start and end of each line

  • Applies to visualise_single_sequence(), visualise_many_sequences(), and visualise_methylation()

  • Controlled via index_annotation_always_first_base and index_annotation_always_last_base logical arguments.

  • On by default

• visualise_methylation() can now draw text inside the boxes

  • Can draw sequence text like visualise_many_sequences(), via sequence_text_type = "sequence".

  • Can draw sequence probabilities, via sequence_text_type = "probability". sequence_text_rounding and sequence_text_scaling then determine how the probability score integers from 0-255 are scaled (e.g. c(-0.5, 256) takes (probability + 0.5) / 256 to convert to 0-1 probability) and rounded for display.

  • As a consequence, visualise_methylation() now takes sequences rather than sequence lengths as its third input, and extract_and_sort_methylation() therefore returns sequences as well as sequence lengths.

• visualise_methylation_colour_scale can now have the text assigned to any of the four cardinal directions rather than always below. If set to "left" / "west" or "right" / "east", gradient direction will be vertical instead of horizontal.

Minor changes:

• visualise_single_sequence(), visualise_many_sequences(), and visualise_methylation() can now use geom_raster() instead of geom_tile() when sequence text, index annotations, and box outlines are off. This provides a moderate performance improvement and can be forced via force_raster = TRUE.

• visualise_single_sequence(), visualise_many_sequences(), visualise_methylation(), and visualise_methylation_colour_scale() all now have a monitor_performance argument which prints the time taken for each step. This is mostly for internal debugging purposes.

• Changed extract_methylation_from_dataframe() to now return a list of 4 vectors instead of 3, with sequences added. sequence_lengths is still returned just in case it’s useful for anything, but it is no longer used in visualise_methylation(), which now takes the sequences directly rather than their lengths.

• Removed warning for “incorrectly” removing index annotations. Now setting any relevant argument to 0/empty (e.g. index_annotation_size = 0, index_annotation_interval = 0, index_annotation_lines = numeric(0)) will automatically change the “main” one to remove annotations.

• read_fastq() and read_modified_fastq() have a strip_at argument to remove leading ’@’s from read IDs via new helper strip_leading_at(). This prevents issues when FASTQ read IDs start with @ but metadata read IDs do not, and IDs therefore cannot be merged.

• Massively improved rasterise_matrix() performance by vectorising calculations.

• Changed default pixels_per_base from 20 to 100 for visualise_methylation() because there is now the option for index and sequence text, which requires a higher resolution to be legible.

• Added accessible palette to sequence_colour_palettes.

• Starting changing all argument validation to use bad_arg().

• Enforced version requirement for ggplot2 (>= 4.0.0).

Full list of new functions, including exported helpers:

• ggDNAvis_shinyapp

• extract_and_sort_methylation() - renamed from extract_methylation_from_dataframe() for consistency with extract_and_sort_sequences(), though the old name still works as an alias.

• bad_arg() - throws an error with information (e.g. name, class, value) about a problematic argument.

• strip_leading_at() - strips leading @ from elements of character vector (e.g. read IDs)

• resolve_alias() - resolves value of an argument where aliases are used.

• resolve_alias_map() - processes a list of many potential aliases for various arguments of a function, using resolve_alias() for each individually.

• monitor_start() - initiate performance monitoring.

• monitor() - continue performance monitoring.

• format_time_diff() - format a difference between times.

• convert_sequences_to_matrix() - convert vector of sequences to character matrix.

• insert_at_indices() - inserts blank lines for index annotations.

• rasterise_index_annotations() - calculates coordinates and labels for index annotations.

• rasterise_probabilities() - calculates coordinates and labels for methylation probabilities.

Deleted functions:

• convert_input_seq_to_sequence_list()

• convert_sequences_to_annotations()

ggDNAvis 0.3.2

• Added files related to pkgdown website building to .Rbuildignore so they are not part of the R package anymore (this caused a CRAN rejection).

ggDNAvis 0.3.1

Bug fixes:

• Fixed 1-pixel-wide border appearing between the panel and the margin when using non-white background colours

ggDNAvis 0.3.0

Changes:

• Removed raster::raster() dependency

• Added new rasterise_matrix() function to do rasterisation

• Changed convert_input_seq_to_sequence_list() behaviour:

  • Instead of additional spacing lines always being added before or after first line of sequence, there are now independent boolean settings for whether there should be spacing lines before and whether there should be spacing lines after.

Bug fixes:

• Fixed critical error with plot matching lenience on some local linux systems that resulted in tests failing

• Inserted additional padding blank lines above/below with index_annotation_vertical_position > 1 to avoid plot dimensions breaking (visualise_single_sequence())

Known issues remaining:

• Related to ggplot v4.0.0:

  • Pixel rendering changes means rectangles sometimes fail to render in visualise_methylation_colour_scale(), resulting in the appearance of vertical white lines. This depends on the precision and exact export size.

  • There is a faint line around the panel area with non-white backgrounds.

ggDNAvis 0.2.1

• Documented that debug_join_vector_num() and debug_join_vector_str() do not return a value

• Changed some reference images to account for ggplot2 updating to v4.0.0

ggDNAvis 0.2.0

• Initial CRAN submission

• Initial functionality:

  • Visualise single DNA sequences, multiple DNA sequences, and DNA modification (e.g. methylation): visualise_single_sequence(), visualise_many_sequences(), visualise_methylation()

  • Read and write FASTQ, including modified FASTQ produced with -T MM,ML that stores modification information in the header rows: read_fastq(), write_fastq(), read_modified_fastq(), write_modified_fastq()

  • Intelligently merge with metadata including read direction, and reverse all information for reverse reads only to make all reads “forward” versions: merge_fastq_with_metadata(), merge_methylation_with_metadata()