threePanelPlot: Visualize cytometry data

In prada: Data analysis for cell-based functional assays

Description

Function to visualize multivariate (cytometry) data in three two-dimensional plots.

Usage

threePanelPlot(data, x.panels = c(1, 4, 5), y.panels = c(2, 3, 6),
               tot.width = 15, tot.height = 5.4, maxcells = 20000,
               limits = c(0, 1023), remove.extremes = TRUE,
               plotTitle = "Three-Panel Plot", use.smoothScatter = TRUE,
               palette = colorRampPalette(brewer.pal(9, "Blues")),
               new.device = TRUE, verbose = TRUE,
               addPoints = NULL, addCol = "red", ...)

Arguments

data	data matrix to visualize
x.panels	which variables (columns) are to be plotted at the x-axis of the three variables
y.panels	which variables (columns) are to be plotted at the y-axis of the three variables
tot.width	width of a new device to open, see argument new.device
tot.height	height of a new device to open, see argument new.device
maxcells	maximum number of observations (cells) for plotting; higher numbers reduce performance
limits	minimum and maximum value (theoretically) observed in the data; e.g., with 10-channel digitized data it is c(0,1023)
remove.extremes	logical; are extreme values (equal to theoretical limits) to be removed before plotting
plotTitle	title for the plot
use.smoothScatter	logical, should the function smoothScatter be employed for plotting the data (plots data densities rather than individual points)
palette	if smoothScatter is used, which colour palette is it to use
new.device	logical; should a new device be opened for the three plots; if FALSE the three plots will be plotted to the currently active device
verbose	logical; do you want extended output to STDOUT
addPoints	should special points be marked after plotting the data; is expected to be a subser of argument data with the same number of columns (=variables); if NULL no points are marked
addCol	in which colour are the points in addPoints to be marked
...	further arguments passed on to plot.default

Value

no value is returned; the function is called to produce three plots

Author(s)

Joern Toedling [e-mail]

See Also

plot.default

Examples

   # generate some data:
   toyData <- cbind(matrix(pmax(0,pmin(runif(3000)+rnorm(3000),4)),ncol=3),
                    matrix(pmax(0,pmin(rnorm(3000,2,1),4)),ncol=3))
   colnames(toyData) <- paste("Var",1:6,sep="")
   toyQuantiles <- apply(toyData,2,quantile,probs=c(0.25,0.5,0.75))

   # plot it and mark the quantiles:
   threePanelPlot(toyData,addPoints=toyQuantiles,
                  addCol=c("orange","red","purple"),limits=c(0,4),pch=20)

prada documentation built on April 28, 2020, 7:52 p.m.