smoothScatter {geneplotter} | R Documentation |
smoothScatter
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=NULL, nbin=128, bandwidth, colramp=colorRampPalette(c("white", brewer.pal(9, "Blues"))), nrpoints=100, transformation=function(x) x^.25, xlab=NULL, ylab=NULL, postPlotHook=box, pch=".", cex=1, xlim, ylim, col="black", xaxs=par("xaxs"), yaxs=par("yaxs"), ...) densCols(x, y=NULL, 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 the 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. The first nrpoints points
from those areas of lowest regional densities will be plotted. Adding
points to the plot allows for the identification of outliers.
If all points are to be plotted, choose nrpoints = Inf . |
transformation |
Function that maps the density scale to the color scale. |
xlab, ylab |
Character. Gets passed on to image |
postPlotHook |
Either NULL or a function with no
arguments that will be called after image . |
pch |
points parameter setting |
cex |
character expansion parameter setting
(see par ) passed to the points phase
of the function |
xlim, ylim |
Numeric vectors of length 2, axis limits. |
col |
points color parameter |
xaxs, yaxs, ... |
Further arguments that are passed on to image . |
These functions are convenience wrappers around
bkde2D
.
The treatment of the x
and y
arguments attempts to be
consistent with that e.g. of plot.default
.
See examples for how to use this function together withn pairs
.
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>
x1 <- matrix(rnorm(1e4), ncol=2) x2 <- matrix(rnorm(1e4, mean=3, sd=1.5), ncol=2) x <- rbind(x1,x2) oldpar <- par(mfrow=c(2,2)) smoothScatter(x, nrpoints=0) smoothScatter(x) smoothScatter(x,nrpoints=Inf,colramp=colorRampPalette(RColorBrewer::brewer.pal(9, "YlOrRd")),bandwidth=1) colors <- densCols(x) plot(x, col=colors, pch=20) ## use with pairs: par(mfrow=c(1,1)) y <- matrix(rnorm(40000), ncol=4) + 3*rnorm(10000) y[, c(2,4)] <- (-y[, c(2,4)]) pairs(y, panel=function(...) {par(new=TRUE);smoothScatter(..., nrpoints=0)}) par(oldpar)