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
.
## 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", ...)
x |
|
y |
Numeric or character vector of length 2 indicating the channels to plot. |
nlevels |
The approximate number of contour line levels, see
|
bw |
The bandwidth factor used for the kernel density estimation, see
|
grid.size |
The grid size used for the kernel density estimation, see
|
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. |
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.
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.
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)