ggDNAvis aliases

As of v1.0.0, ggDNAvis supports function and argument aliases. The code is entirely written with British spellings (e.g. visualise_methylation_colour_scale()), but should also accept American spellings (e.g. visualize_methylation_color_scale()). If any American spellings don't work, I most likely overlooked them and can easily fix, so please submit a bug report by creating a github issue (https://github.com/ejade42/ggDNAvis/issues).

All four major visualise_ functions have aliases to also accept visualize_:

• visualise_many_sequences() (visualize_many_sequences())

• visualise_methylation() (visualize_methylation())

• visualise_methylation_colour_scale() (visualize_methylation_color_scale())

• visualise_single_sequence() (visualize_single_sequence())

As of v1.0.0, extract_methylation_from_dataframe() has been renamed extract_and_sort_methylation() for consistency with extract_and_sort_sequences(). To preserve compatibility and ensure consistency, both functions now accept either name formulation:

• extract_and_sort_sequences() (extract_sequences_from_dataframe())

• extract_and_sort_methylation() (extract_methylation_from_dataframe())

The builtin dataset sequence_colour_palettes, like all colour arguments, also accepts color or col:

• sequence_colour_palettes (sequence_color_palettes & sequence_col_palettes)

The interactive shinyapp can be called via ggDNAvis_shinyapp() or ggDNAvis_shiny().

Additionally, the three rasterise_ helper functions also accept rasterize_:

• rasterise_matrix() (rasterize_matrix())

• rasterise_index_annotations() (rasterize_index_annotations())

• rasterise_probabilities() (rasterize_probabilities())

All arguments should have aliases configured. In particular, any _colour arguments should also accept _color or _col.

When more than one equivalent argument is provided, the 'canonical' (British) argument takes precedence, and will produce a warning message explaining this. For colours, _colour takes precedence over _color, which itself takes precedence over _col.

I have also tried to provide aliases for common argument misspellings. In particular, index_annotation_full_line also accepts any of index_annotations_full_lines, index_annotation_full_lines, or index_annotations_full_line. Likewise, index_annotations_above also accepts index_annotation_above.

Examples

d <- extract_methylation_from_dataframe(example_many_sequences)
## The resulting low colour will be green
visualise_methylation(
    d$locations,
    d$probabilities,
    d$sequences,
    index_annotation_lines = NA,
    outline_linewidth = 0,
    high_colour = "white",
    low_colour = "green",
    low_color = "orange",
    low_col = "purple"
)
#> Warning: Both 'low_colour' and alias 'low_color' were provided.
#> 'low_color' will be discarded.
#>     Value: orange
#> 'low_colour' will be used.
#>     Value: green
#> Warning: Both 'low_colour' and alias 'low_col' were provided.
#> 'low_col' will be discarded.
#>     Value: purple
#> 'low_colour' will be used.
#>     Value: green
#> ℹ Automatically using geom_raster (much faster than geom_tile) as no sequence text, index annotations, or outlines are present.
#> Warning: When using geom_raster, it is recommended to use a smaller pixels_per_base e.g. 10, as there is no text/outlines that would benefit from higher resolution.
#> Current value: 100


## The resulting low colour will be orange
visualise_methylation(
    d$locations,
    d$probabilities,
    d$sequences,
    index_annotation_lines = NA,
    outline_linewidth = 0,
    high_colour = "white",
    low_color = "orange",
    low_col = "purple"
)
#> Warning: Both 'low_colour' and alias 'low_color' were provided.
#> 'low_color' will be discarded.
#>     Value: orange
#> 'low_colour' will be used.
#>     Value: purple
#> ℹ Automatically using geom_raster (much faster than geom_tile) as no sequence text, index annotations, or outlines are present.
#> Warning: When using geom_raster, it is recommended to use a smaller pixels_per_base e.g. 10, as there is no text/outlines that would benefit from higher resolution.
#> Current value: 100


## The resulting low colour will be purple
visualise_methylation(
    d$locations,
    d$probabilities,
    d$sequences,
    index_annotation_lines = NA,
    outline_linewidth = 0,
    high_colour = "white",
    low_col = "purple"
)
#> ℹ Automatically using geom_raster (much faster than geom_tile) as no sequence text, index annotations, or outlines are present.
#> Warning: When using geom_raster, it is recommended to use a smaller pixels_per_base e.g. 10, as there is no text/outlines that would benefit from higher resolution.
#> Current value: 100