auxil: Auxiliary functions for adegenet

In adegenet: Exploratory Analysis of Genetic and Genomic Data

Auxiliary functions for adegenet

Description

adegenet implements a number of auxiliary procedures that might be of interest for users. These include graphical tools to translate variables (numeric or factors) onto a color scale, adding transparency to existing colors, pre-defined color palettes, extra functions to access documentation, and low-level treatment of character vectors.

These functions are mostly auxiliary procedures used internally in adegenet.

These items include:

• num2col: translates a numeric vector into colors.

• fac2col: translates a factor into colors.

• any2col: translates a vector of type numeric, character or factor into colors.

• transp: adds transparency to a vector of colors. Note that transparent colors are not supported on some graphical devices.

• corner: adds text to a corner of a figure.

• checkType: checks the type of markers being used in a function and issues an error if appropriate.

• .rmspaces: remove peripheric spaces in a character string.

• .genlab: generate labels in a correct alphanumeric ordering.

• .readExt: read the extension of a given file.

Color palettes include:

• bluepal: white -> dark blue

• redpal: white -> dark red

• greenpal: white -> dark green

• greypal: white -> dark grey

• flame: gold -> red

• azur: gold -> blue

• seasun: blue -> gold -> red

• lightseasun: blue -> gold -> red (light variant)

• deepseasun: blue -> gold -> red (deep variant)

• spectral: red -> yellow -> blue (RColorBrewer variant)

• wasp: gold -> brown -> black

• funky: many colors

• virid: adaptation of the viridis palette, from the viridis package.

• hybridpal: reorder a color palette (virid by default) to display sharp contrast between the first two colors, and interpolated colors after; ideal for datasets where two parental populations are provided first, followed by various degrees of hybrids.

Usage

.genlab(base, n)
corner(text, posi="topleft",  inset=0.1, ...)
num2col(x, col.pal=heat.colors, reverse=FALSE,
        x.min=min(x,na.rm=TRUE), x.max=max(x,na.rm=TRUE),
        na.col="transparent")
fac2col(x, col.pal=funky, na.col="transparent", seed=NULL)
any2col(x, col.pal=seasun, na.col="transparent")
transp(col, alpha=.5)
hybridpal(col.pal = virid)

Arguments

base	a character string forming the base of the labels
n	the number of labels to generate
text	a character string to be added to the plot
posi	a character matching any combinations of "top/bottom" and "left/right".
inset	a vector of two numeric values (recycled if needed) indicating the inset, as a fraction of the plotting region.
...	further arguments to be passed to text
x	a numeric vector (for num2col) or a vector converted to a factor (for fac2col).
col.pal	a function generating colors according to a given palette.
reverse	a logical stating whether the palette should be inverted (TRUE), or not (FALSE, default).
x.min	the minimal value from which to start the color scale
x.max	the maximal value from which to start the color scale
na.col	the color to be used for missing values (NAs)
seed	a seed for R's random number generated, used to fix the random permutation of colors in the palette used; if NULL, no randomization is used and the colors are taken from the palette according to the ordering of the levels.
col	a vector of colors
alpha	a numeric value between 0 and 1 representing the alpha coefficient; 0: total transparency; 1: no transparency.

Value

For .genlab, a character vector of size "n". num2col and fac2col return a vector of colors. any2col returns a list with the following components: $col (a vector of colors), $leg.col (colors for the legend), and $leg.txt (text for the legend).

Author(s)

Thibaut Jombart [e-mail]

See Also

The R package RColorBrewer, proposing a nice selection of color palettes. The viridis package, with many excellent palettes.

Examples

.genlab("Locus-",11)

## transparent colors using "transp"
plot(rnorm(1000), rnorm(1000), col=transp("blue",.3), pch=20, cex=4)


## numeric values to color using num2col
plot(1:100, col=num2col(1:100), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=bluepal), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=flame), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=wasp), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=azur,rev=TRUE), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=spectral), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=virid), pch=20, cex=4)

## factor as colors using fac2col
dat <- cbind(c(rnorm(50,8), rnorm(100), rnorm(150,3),
rnorm(50,10)),c(rnorm(50,1),rnorm(100),rnorm(150,3), rnorm(50,5)))
fac <- rep(letters[1:4], c(50,100,150,50))
plot(dat, col=fac2col(fac), pch=19, cex=4)
plot(dat, col=transp(fac2col(fac)), pch=19, cex=4)
plot(dat, col=transp(fac2col(fac,seed=2)), pch=19, cex=4)

## use of any2col
x <- factor(1:10)
col.info <- any2col(x, col.pal=funky)
plot(x, col=col.info$col, main="Use of any2col on a factor")
legend("bottomleft", fill=col.info$leg.col, legend=col.info$leg.txt, bg="white")

x <- 100:1
col.info <- any2col(x, col.pal=wasp)
barplot(x, col=col.info$col, main="Use of any2col on a numeric")
legend("bottomleft", fill=col.info$leg.col, legend=col.info$leg.txt, bg="white")

adegenet documentation built on Feb. 16, 2023, 6 p.m.