contour-methods {flowViz} | R Documentation

## Contour plots for flow data

### Description

Basic contour plots for both `flowFrame`s and `flowSet`s. The densities for the contours are estimated using the fast kernel density estimation algorithm `bkde2D`.

### Usage

    ## method for 'flowFrame' objects
    ## S4 method for signature 'flowFrame':
    contour(
        x,
        y=1:2,
        nlevels=10,
        bw,
        grid.size=c(65,65),
        add=FALSE,
        xlab,
        ylab,
        lwd=1,
        lty=1,
        col=par("fg"),
        fill="transparent",
        ...)

    ## method for 'flowSet' objects
    ## S4 method for signature 'flowSet':
    contour(
        x,
        y=1:2,
        add=FALSE,
        xlab,
        ylab,
        lwd=1,
        lty=1,
        col=par("fg"),
        fill="transparent",
        ...)

### Arguments

`x` | An object of class `flowFrame` or `flowSet`.
`y` | Numeric or character vector of length 2 indicating the channels to plot.
`nlevels` | The approximate number of contour line levels, see `contour` for details.
`bw` | The bandwidth factor used for the kernel density estimation, see `bkde2D` for details.
`grid.size` | The grid size used for the kernel density estimation, see `bkde2D` for details.
`add` | Logical, indicating whether contour lines should be superimposed on an existing plot.
`xlab, ylab` | The axis annotation.
`lwd, lty, col, fill` | The usual plotting parameters, i.e. the line width, line type, line color and fill color. When using a fill color you should consider alpha blending to improve the results.
`...` | Parameters that are passed on to the plotting functions.

### Methods

x = "flowFrame"
  A regular contour plot of the flow data in the frame. It can be added on top of an existing plot using the `add` argument.
x = "flowSet"
  Overlay of contours of densities for each individual frame in the set. You should consider using differnt colors and alpha blending to improve the result. This is only useful for a very limited number of frames in a set (~5), for larger sets you should consider a panelled lattice-type plot. Not that `bw`, `gridSize` and `nlevels` are passed on via the ... argument.

### Author(s)

F. Hahne

### See Also

`bkde2D`, `contour`, `flowFrame`, `flowSet`

### Examples

    data(GvHD)

    ## simple contour plot
    contour(GvHD[[1]])

    ## overlay with existing plot
    plot(GvHD[[1]], c("FSC-H", "SSC-H"))
    contour(GvHD[[1]], add=TRUE, col="lightgray", lty=3)

    ## colored contours
    contour(GvHD[[1]], fill="red")
    cols <- rainbow(3, alpha=0.1)
    contour(GvHD[[1]], fill=cols, col=cols)

    ## overlay of multiple flowFrames in a flowSet
    contour(GvHD[1:3], col=cols, fill=cols)

[Package flowViz version 1.6.2 Index]