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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(flowViz)
Loading required package: flowCore
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowViz/contour-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: contour-methods
> ### Title: Contour plots for flow data
> ### Aliases: contour contour,ANY-method contour,flowFrame-method
> ### contour,flowSet-method contour-methods
> ### Keywords: methods
>
> ### ** 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)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
