adegenet (version 1.3-5)

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, with the exception of, which opens the adegenet website in the default navigator. These items include: - adegenetWeb: opens the adegenet website in a web navigator - num2col: translates a numeric vector into colors. - fac2col: translates a numeric vector 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->blue - redpal: white->red - greenpal: white->green - flame: gold->red - seasun: blue->gold->red - lightseasun: blue->gold->red (light variant) - deepseasun: blue->gold->red (deep variant) - funky: many colors

Usage

adegenetWeb()
.genlab(base, n)
corner(text, posi="topleft",  inset=0.1, ...)
num2col(x, col.pal=heat.colors, reverse=FALSE,
               x.min=min(x), x.max=max(x), na.col="green")
fac2col(x, col.pal=funky, na.col="grey", seed=1)
transp(col, alpha=.5)

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.

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".

encoding

UTF-8

Examples

## this opens the adegenet website
adegenetWeb()

.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=seasun), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=seasun,rev=TRUE), 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)