Colour palettes for sequence visualisations

sequence_color_palettes and sequence_col_palettes are aliases for sequence_colour_palettes - see aliases.

A collection of colour palettes for use with visualise_single_sequence() and visualise_many_sequences(). Each is a character vector of 4 colours, corresponding to A, C, G, and T/U in that order.

To use inside the visualisation functions, set sequence_colours = sequence_colour_palettes$<palette_name>

Generation code is available at data-raw/sequence_colour_palettes.R

Usage

sequence_colour_palettes

Format

sequence_colour_palettes

A list of 6 length-4 character vectors

ggplot_style

The shades of red, green, blue, and purple that ggplot2::ggplot() uses by default for a 4-way discrete colour scheme.

Values: c("#F8766D", "#7CAE00", "#00BFC4", "#C77CFF")

bright_pale

Bright yellow, green, blue, and red in lighter pastel-like tones.

Values: c("#FFDD00", "#40C000", "#00A0FF", "#FF4E4E")

bright_pale2

Bright yellow, green, blue, and red in lighter pastel-like tones. The green (for C) is slightly lighter than bright_pale.

Values: c("#FFDD00", "#30EC00", "#00A0FF", "#FF4E4E")

bright_deep

Bright orange, green, blue, and red in darker, richer tones.

Values: c("#FFAA00", "#00BC00", "#0000DC", "#FF1E1E")

sanger

Green, blue, black, and red similar to a traditional Sanger sequencing readout.

Values: c("#00B200", "#0000FF", "#000000", "#FF0000")

accessible

Light green, dark green, dark blue, and light blue as suggested by colorbrewer2.org for a 4-qualitative-category colourblind-safe palette.

Values: c("#B2DF8A", "#33A02C", "#1F78B4", "#A6CEE3")

Examples

## ggplot_style:
visualise_single_sequence(
    "ACGT",
    sequence_colours = sequence_colour_palettes$ggplot_style,
    index_annotation_interval = 0
)
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_first_base setting.
#> If you want the first base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_last_base setting.
#> If you want the last base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.


## bright_pale:
visualise_single_sequence(
    "ACGT",
    sequence_colours = sequence_colour_palettes$bright_pale,
    index_annotation_interval = 0
)
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_first_base setting.
#> If you want the first base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_last_base setting.
#> If you want the last base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.


## bright_pale2:
visualise_single_sequence(
    "ACGT",
    sequence_colours = sequence_colour_palettes$bright_pale2,
    index_annotation_interval = 0
)
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_first_base setting.
#> If you want the first base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_last_base setting.
#> If you want the last base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.


## bright_deep:
visualise_single_sequence(
    "ACGT",
    sequence_colours = sequence_colour_palettes$bright_deep,
    sequence_text_colour = "white",
    index_annotation_interval = 0
)
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_first_base setting.
#> If you want the first base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_last_base setting.
#> If you want the last base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.


## sanger:
visualise_single_sequence(
    "ACGT",
    sequence_colours = sequence_colour_palettes$sanger,
    sequence_text_colour = "white",
    index_annotation_interval = 0
)
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_first_base setting.
#> If you want the first base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_last_base setting.
#> If you want the last base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.


## accessible:
visualise_single_sequence(
    "ACGT",
    sequence_colours = sequence_colour_palettes$accessible,
    sequence_text_colour = "black",
    index_annotation_interval = 0
)
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_first_base setting.
#> If you want the first base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.
#> Warning: Disabling index annotations via index_annotation_interval = 0 or index_annotation_size = 0 overrides the index_annotation_always_last_base setting.
#> If you want the last base in each line to be annotated but no other bases, set index_annotation_interval greater than line_wrapping.