coloring: XString Display Colors

In Bioconductor/Biostrings: Efficient manipulation of biological strings

XString Display Colors

Description

XString objects support custom coloring for display. Users can also set custom color palettes for XString objects using the update_X_palette functions.

Usage

update_DNA_palette(colors=NULL)
update_RNA_palette(colors=NULL)
update_AA_palette(colors=NULL)
update_B_palette(colors=NULL)

Arguments

colors

A named list of colors to update, with entries fg and bg specifying the foreground and background colors, respectively. Colors can be specified in any way compatible with make_style from the crayon package. Defaults to NULL, which resets the color palette to the default color scheme. See Details and Examples for more information.

Details

XString objects support the following default coloring for display.

• DNAString: A, C, G, and T are colored red, green, blue, and orange (respectively), N is colored light grey, other ambiguity codes are colored dark grey, and "-+." have no coloring.

• RNAString: All bases are colored identically to DNAString. U is colored yellow.

• AAString: Amino acids are colored according to JalView's Zappo color scheme, representing physicochemical properties. X is colored light grey, other ambiguity codes are colored dark grey, and "*-+." are not colored.

• BStrings are not colored.

Users can change the default color scheme of Biostrings with the update_X_palette family functions. Each function expects a list with named entries corresponding to the values to update. Each entry can specify 'fg' and 'bg' values, corresponding to the foreground and background colors (respectively). If 'fg' is not specified, it defaults to rgb(1,1,1) (white). If 'bg' is not specified, it defaults to transparent.

These functions will only update the values passed, leaving the rest of the colors as-is. For example, calling update_AA_palette(list(A=list(fg="green"))) would update the coloring for A while leaving all other colors as the default schema.

To reset all colors to the default palette, call the function with no arguments (NULL).

To remove a coloring for a specific value, provide a named entry with value NULL. For example, update_AA_palette(list(A=NULL)) will remove the coloring for A.

update_DNA_palette and update_RNA_palette are identical internally, so either function can be used to update colorings for T,U.

See the Examples section for more examples of custom colorings.

Value

For update_X_palette, Invisibly returns the new color mapping, consisting of a named character vector. Calling cat on the return value will print out all letters with their respective coloring.

Author(s)

Aidan Lakshman <[e-mail]>

See Also

XString-class

Examples

## display default colors
DNAString(paste(DNA_ALPHABET, collapse=''))
RNAString(paste(RNA_ALPHABET, collapse=''))
AAString(paste(AA_ALPHABET, collapse=''))
BString(paste(LETTERS, collapse=''))

## create new palettes
DNA_palette <- list(
  A=list(fg="blue",bg="black"),
  T=list(fg="red",bg='black'),
  G=list(fg='green',bg='black'),
  C=list(fg='yellow',bg='black')
)
update_DNA_palette(DNA_palette)
DNAString(paste(DNA_ALPHABET, collapse=''))

## reset to default palette
update_DNA_palette()
DNAString(paste(DNA_ALPHABET, collapse=''))

## colors can also be specified with `rgb()`
AA_palette <- list(
  A=list(fg="white", bg="purple"),
  B=list(fg=rgb(1,1,1), bg='orange')
)
update_AA_palette(AA_palette)
AAString(paste(AA_ALPHABET, collapse=''))

## remove all coloring for QEG
update_AA_palette(list(Q=NULL, E=NULL, G=NULL))
AAString(paste(AA_ALPHABET, collapse=''))

## reset to default
update_AA_palette()
AAString(paste(AA_ALPHABET, collapse=''))

## We can also add colors to BStrings,
## which are normally not colored

## if 'fg' is not specified, defaults to rgb(1,1,1)
## if 'bg' is not specified, background is transparent
B_palette <- list(
  A=list(bg='green'),
  B=list(bg="red"),
  C=list(bg='blue'),
  D=list(fg="orange"),
  E=list(fg="yellow")
)
update_B_palette(B_palette)
BString(paste(LETTERS, collapse=''))

## can also directly view the changes with cat
cat(update_B_palette(B_palette), '\n')

## reset to default
update_B_palette()
BString(paste(LETTERS, collapse=''))

Bioconductor/Biostrings documentation built on Feb. 24, 2025, 8:59 a.m.