Changelog

Source: NEWS.md

ggDNAvis (development version)

New features:

• 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.

• visualise_methylation() now has the ability to draw sequence and probability text!

• All function, argument, and data names now have aliases i.e. accept American spellings

  • 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_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.

User-facing changes:

• 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.

• 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.

New helper functions:

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

• insert_at_indices() - inserts blank lines for index annotations in visualise_many_sequences() and visualise_methylation().

• create_many_sequence_index_annotations() - calculates coordinates and labels for index annotations in visualise_many_sequences() and visualise_methylation().

Background changes:

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

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

ggDNAvis 0.3.2

CRAN release: 2025-10-31

• 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

CRAN release: 2025-10-01

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

CRAN release: 2025-09-21

• 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()