threePanelPlot {prada}R Documentation

Visualize cytometry data

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 toedling@ebi.ac.uk

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)

[Package prada version 1.8.0 Index]