panel.smoothScatter {geneplotter} | R Documentation

## Lattice panel function analogous to smoothScatter

### Description

This function allows the user to place `smoothScatter` plots into lattice graphics.

### Usage

    panel.smoothScatter(x, y = NULL,
                        nbin = 64, cuts = 255,
                        bandwidth,
                        colramp =
                        colorRampPalette(c("white", brewer.pal(9, "Blues"))),
                        nrpoints = 100,
                        transformation = function(x) x^0.25,
                        pch = ".",
                        cex = 1, col="black",
                        range.x,
                        ...,
                        subscripts)

### 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.
`cuts` | number of cuts defining the color gradient
`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.
`pch, cex` | graphical parameters for the `nrpoints` “outlying” points shown in the display
`range.x` | see `bkde2D` for details.
`col` | `points` color parameter
`...` | Further arguments that are passed on to `panel.levelplot`.
`subscripts` | ignored, but necessary for handling of ... in certain situations. Likely to be removed in future.

### Details

This replicates the display part of the `smoothScatter` function by replacing standard graphics calls by grid-compatible ones.

### Value

The function is called for its side effects, namely the production of the appropriate plots on a graphics device.

### Author(s)

Deepayan Sarkar deepayan.sarkar@r-project.org

### See Also

`smoothScatter`

### Examples

    ddf <- as.data.frame(matrix(rnorm(40000), ncol = 4) + 3 * rnorm(10000))
    ddf[, c(2,4)] <- (-ddf[, c(2,4)])
    xyplot(V1 ~ V2 + V3, ddf, outer = TRUE,
           panel = panel.smoothScatter, aspect = "iso")
    splom(ddf, panel = panel.smoothScatter, nbin = 64)

[Package geneplotter version 1.20.0 Index]