threePanelPlot {prada} | R Documentation |
Function to visualize multivariate (cytometry) data in three two-dimensional plots.
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", ...)
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 |
no value is returned; the function is called to produce three plots
Joern Toedling toedling@ebi.ac.uk
# 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)