getBioColor: Color scheme getter for biological data
In biovizBase: Basic graphic utilities for visualization of genomic data.

Description Usage Arguments Details Value Author(s) Examples

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

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"))

`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.

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.

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.

Tengfei Yin

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]