getBioColor: Color scheme getter for biological data

Description

This function tries to get default color scheme either from fixed palette or options for specified data set, usually just biological data.

Usage

getBioColor(type = c("DNA_BASES_N", "DNA_BASES", "DNA_ALPHABET", "RNA_BASES_N", "RNA_BASES", "RNA_ALPHABET", "IUPAC_CODE_MAP", "AMINO_ACID_CODE", "AA_ALPHABET", "STRAND", "CYTOBAND"), source = c("option", "default"))

Arguments

type

Color set based on which you want to get.

source

"option" tries to get color scheme from Options. This allow user to edit the color globally. "default" gets fixed color scheme.

Value

A character of vector contains color(rgb), and the names of the vector is originally from the name of different data set. e.g. for DNA_BASES, it's just A,C,T,G. This allow users to get color for a vector of specified names. Please see the examples below.

Details

Most data set specified in the type argument are defined in Biostrings package, such as "DNA_BASES", "DNA_ALPHABET", "RNA_BASES", "RNA_ALPHABET", "IUPAC_CODE_MAP", "AMINO_ACID_CODE", "AA_ALPHABET", please check the manual for more details.

"DNA_BASES_N" is just "DNA_BASES" with extra "N" used in certain cases, like the result from applyPileup in Rsamtools package. We start with the five most used nucleotides, A,T,C,G,N, In genetics, GC-content usually has special biological significance because GC pair is bound by three hydrogen bonds instead of two like AT pairs. So it has higher thermostability which could result in different significance, like higher annealing temperature in PCR. So we hope to choose warm color for G,C and cold color for A,T, and a color in between to represent N. They are chosen from diverging color set of color brewer. So we should be able to easily tell the GC enriched region. This set of color also passed vischeck for colorblind people.

In GRanges object, we have strand which contains three levels, +, -, *. We are using a qualitative color set from Color Brewer. This color set pass the colorblind test. It should be a safe color set to use to color strand.

For most default color scheme if they are under 18, we are trying to use package dichromat to set color for color blind people. But for data set that contains more than 18 objects, it's not possible to assign colorblind-safe color to them anymore. So we need to repeat some color. It should not matter too much, because even normal people cannot tell the difference anymore.

Here are the definition for the data sets.

DNA_BASES: Contains A,C,T,G.

DNA_ALPHABET

This alphabet contains all letters from the IUPAC Extended Genetic Alphabet (see "?IUPAC_CODE_MAP") + the gap ("-") and the hard masking ("+") letters.

DNA_BASES_N

Contains A,C,T,G,N

RNA_BASES_N

Contains A,C,U,G,N

RNA_BASES

Contains A,C,T,G

RNA_ALPHABET

This alphabet contains all letters from the IUPAC Extended Genetic Alphabet (see ?IUPAC_CODE_MAP) where "T" is replaced by "U" + the gap ("-") and the hard masking ("+") letters.

IUPAC_CODE_MAP

The "IUPAC_CODE_MAP" named character vector contains the mapping from the IUPAC nucleotide ambiguity codes to their meaning.

AMINO_ACID_CODE

Single-Letter Amino Acid Code (see "?AMINO_ACID_CODE").

AA_ALPHABET

This alphabet contains all letters from the Single-Letter Amino Acid Code (see "?AMINO_ACID_CODE") + the stop ("*"), the gap ("-") and the hard masking ("+") letters

STRAND

Contains "+", "-", "*"

CYTOBAND

Contains giemsa stain results:

gneg, gpos25, gpos50, gpos75,
	gpos100, gvar, stalk, acen

. Color defined in package geneplotter.

Examples

Run this code

opts <- getOption("biovizBase")
opts$DNABasesNColor[1] <- "red"
options(biovizBase = opts)
## get from option(default)
getBioColor("DNA_BASES_N")
## get default fixed color
getBioColor("DNA_BASES_N", source = "default")
seqs <- c("A", "C", "T", "G", "G", "G", "C")
## get colors for a sequence.
getBioColor("DNA_BASES_N")[seqs]

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