contour-methods {flowViz} | R Documentation |
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
.
## 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", ...)
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. |
add
argument.bw
,
gridSize
and nlevels
are passed on via the ...
argument.
F. Hahne
bkde2D
, contour
,
flowFrame
,
flowSet
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)