smoothScatter {graphics}

R Documentation

Scatterplots with Smoothed Densities Color Representation

Description

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.

Usage

smoothScatter(x, y = NULL, nbin = 128, bandwidth,
              colramp = colorRampPalette(c("white", blues9)),
              nrpoints = 100, pch = ".", cex = 1, col = "black",
              transformation = function(x) x^.25,
              postPlotHook = box,
              xlab = NULL, ylab = NULL, xlim, ylim,
              xaxs = par("xaxs"), yaxs = par("yaxs"), ...)

Arguments

x, y	the x and y arguments provide the x and y coordinates for the plot. Any reasonable way of defining the coordinates is acceptable. See the function xy.coords for details. If supplied separately, they must be of the same length.
nbin	numeric vector of length one (for both directions) or two (for x and y separately) specifying the number of equally spaced grid points for the density estimation; directly used as gridsize in bkde2D().
bandwidth	numeric vector (length 1 or 2) of smoothing bandwidth(s). If missing, a more or less useful default is used. bandwidth is subsequently passed to function bkde2D.
colramp	function accepting an integer n as an argument and returning n colors.
nrpoints	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.
pch, cex, col	arguments passed to points, when nrpoints > 0: point symbol, character expansion factor and color, see also par.
transformation	function mapping the density scale to the color scale.
postPlotHook	either NULL or a function which will be called (with no arguments) after image.
xlab, ylab	character strings to be used as axis labels, passed to image.
xlim, ylim	numeric vectors of length 2 specifying axis limits.
xaxs, yaxs, ...	further arguments, passed to image.

Details

smoothScatter produces a smoothed version of a scatter plot. Two dimensional (kernel density) smoothing is performed by bkde2D from package KernSmooth. See the examples for how to use this function together with pairs.

Author(s)

Florian Hahne at FHCRC, originally

See Also

bkde2D from package KernSmooth; densCols which uses the same smoothing computations and blues9 in package grDevices.

Examples

  ## A largish data set
  n <- 10000
  x1  <- matrix(rnorm(n), ncol=2)
  x2  <- matrix(rnorm(n, mean=3, sd=1.5), ncol=2)
  x   <- rbind(x1,x2)

  oldpar <- par(mfrow=c(2,2))
  smoothScatter(x, nrpoints=0)
  smoothScatter(x)

  ## a different color scheme:
  Lab.palette <- colorRampPalette(c("blue", "orange", "red"), space = "Lab")
  smoothScatter(x, colramp = Lab.palette)

  ## somewhat similar, using identical smoothing computations,
  ## but considerably *less* efficient for really large data:
  plot(x, col = densCols(x), 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)

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