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) }