smoothScatter {geneplotter} | R Documentation |

## Scatterplots with smoothed densities color representation

### Description

`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.

### Usage

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)]))

### Arguments

`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` . |

### Details

These functions are convenience wrappers around
`bkde2D`

.

### Value

`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.

### Author(s)

Florian Hahne <f.hahne@dkfz.de>

### See Also

`bkde2D`

### Examples

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)
}

[Package

*geneplotter* version 1.8.0

Index]