contour-methods: Contour plots for flow data

In flowViz: Visualization for flow cytometry

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

## S4 method for signature '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.

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

library(flowCore)
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)

flowViz documentation built on Nov. 8, 2020, 7:53 p.m.