flowViz (version 1.36.2)

contour-methods: 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

## S3 method for class 'flowFrame':
contour(x, y = 1:2, nlevels = 10, bw,
  grid.size = c(65, 65), add = FALSE, xlab, ylab, xlim, ylim, 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.

xlim,ylim

The plotting ranges.

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.

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)