| smoothScatter {geneplotter} | R Documentation |
smmothScatter produces a smoothed color density
representation of the scatterplot, obtained through a kernel
density estimate. densCols produces a vector containing
colors which encode the local densities at each point in a
scatterplot.
smoothScatter(x, y,
nbin = 128,
bandwidth,
colramp = colorRampPalette(c("white", brewer.pal(9, "Blues"))),
nrpoints = 100,
transformation = function(x) x^.25,
xlab, ylab, ...)
densCols(x, y,
nbin = 128,
bandwidth,
colramp = colorRampPalette(brewer.pal(9, "Blues")[-(1:3)]))
x |
Numeric vector containing x-values or n by 2 matrix containing x and y values. |
y |
Numeric vector containing y-values (optional). The length of x
must be the same as that of y. |
nbin |
Numeric vector of length 1 (for both directions) or 2 (for x and y separately) containing the number of equally spaced grid points for the density estimation. |
bandwidth |
Numeric vector: the smoothing bandwidth. If missing,
these functions come up with a more or less useful guess. This
parameter then gets passed on to function.
bkde2D. |
colramp |
Function accepting an integer n as an argument and
returning n colors. |
nrpoints |
Numeric vector of length 1 giving number of points to
be superimposed on the density image.
If all points are to be plotted, choose nrpoints = Inf. |
transformation |
Function that maps the density scale to the color scale. |
xlab |
Character. Gets passed on to image |
ylab |
Character. Gets passed on to image |
... |
Further arguments that are passed on to image. |
These functions are convenience wrappers around
bkde2D.
smoothScatter is called for its side-effect, producing a
plot on the current graphics device. densCols returns
a vector of length nrow(x) that contains colors to be used
in a subsequent scatterplot. Each color represents the local density
around the corresponding point.
Florian Hahne <f.hahne@dkfz.de>
if(interactive()) {
x1 <- matrix(rnorm(1e4), ncol=2)
x2 <- matrix(rnorm(1e4, mean=3, sd=1.5), ncol=2)
x <- rbind(x1,x2)
layout(matrix(1:4, ncol=2, byrow=TRUE))
smoothScatter(x, nrpoints=0)
smoothScatter(x)
smoothScatter(x, nrpoints=Inf, colramp=colorRampPalette(RColorBrewer::brewer.pal(9, "YlOrRd")), bandwidth=40)
colors <- densCols(x)
plot(x, col=colors, pch=20)
}