contour-methods: Contour plots for flow data In flowViz: Visualization for flow cytometry

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

 ```1 2 3 4``` ```## 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

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

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16``` ```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) ```

Example output

```Loading required package: flowCore