DEFAULT_COLORS: Default colors

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Default colors

Description

Default color palettes for DNA characters, Ig isotypes, and TCR chains.

Usage

DNA_COLORS

IG_COLORS

TR_COLORS

Format

Named character vectors with hexcode colors as values.

• DNA_COLORS: DNA character colors c("A", "C", "G", "T").

• IG_COLORS: Ig isotype colors c("IGHA", "IGHD", "IGHE", "IGHG", "IGHM", "IGHK", "IGHL").

• TR_COLORS: TCR chain colors c("TRA", "TRB", "TRD", "TRG").

An object of class character of length 4.

An object of class character of length 7.

An object of class character of length 4.

Examples

# IG_COLORS as an isotype color set for ggplot
isotype <- c("IGHG", "IGHM", "IGHM", "IGHA")
db <- data.frame(x=1:4, y=1:4, iso=isotype)
g1 <- ggplot(db, aes(x=x, y=y, color=iso)) + 
    scale_color_manual(name="Isotype", values=IG_COLORS) +
    geom_point(size=10)
plot(g1)

# DNA_COLORS to translate nucleotide values to a vector of colors 
# for use in base graphics plots
seq <- c("A", "T", "T", "C")
colors <- translateStrings(seq, setNames(names(DNA_COLORS), DNA_COLORS))
plot(1:4, 1:4, col=colors, pch=16, cex=6)

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.