Auxiliary functions: 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)

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).

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.

Author

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

Run this code


.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")