Auxiliary functions for adegenet
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.
.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)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 |
x |
a numeric vector (for |
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. |
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 $leg.txt (text for the legend).
Thibaut Jombart t.jombart@imperial.ac.uk
The R package RColorBrewer, proposing a nice selection of color
palettes. The viridis package, with many excellent palettes.
.genlab("Locus-",11)
## transparent colors using "transp"
plot(rnorm(1000), rnorm(1000), col=transp("blue",.3), pch=20, cex=4)
## numeric values to color using num2col
plot(1:100, col=num2col(1:100), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=bluepal), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=flame), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=wasp), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=azur,rev=TRUE), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=spectral), pch=20, cex=4)
plot(1:100, col=num2col(1:100, col.pal=virid), pch=20, cex=4)
## factor as colors using fac2col
dat <- cbind(c(rnorm(50,8), rnorm(100), rnorm(150,3),
rnorm(50,10)),c(rnorm(50,1),rnorm(100),rnorm(150,3), rnorm(50,5)))
fac <- rep(letters[1:4], c(50,100,150,50))
plot(dat, col=fac2col(fac), pch=19, cex=4)
plot(dat, col=transp(fac2col(fac)), pch=19, cex=4)
plot(dat, col=transp(fac2col(fac,seed=2)), pch=19, cex=4)
## use of any2col
x <- factor(1:10)
col.info <- any2col(x, col.pal=funky)
plot(x, col=col.info$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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.