R: Contour plots for flow data

contour-methods {flowViz}

R Documentation

Contour plots for flow data

Description

Basic contour plots for both flowFrames and flowSets. 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

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]