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 1.10.1 Index]