splom {flowViz} | R Documentation

## Method implementing Lattice scatter plot matrices for flow data.

### Description

This function create Trellis scatter plots matrices (splom) from flow cytometry data.

### Usage

    ## S4 method for signature 'flowFrame, missing':
    splom(
        x,
        data,
        pscales,
        time,
        exclude.time=TRUE,
        names=FALSE,
        ...)

    panel.splom.flowframe(
        x,
        frame,
        ...)

### Arguments

`x` | A formula describing the structure of the plot and the variables to be used in the display.
`data, frame` | A `flowFrame` object that serves as the source of data.
`pscales` | This arguments is passed unchanged to the corresponding methods in lattice, and is listed here only because it provides a different default. See documentation for the original methods for details.
`time` | A character string giving the name of the data column recording time. If not provided, we try to guess from the available parameters.
`exclude.time` | Logical, specifying whether to exclude the time variable from a scatter plot matrix. Defaults to `TRUE`.
`names` | Logical specifying wether gate names should be added to the plot. Currently, this feature is not supported for splom plots.
`...` | More arguments, usually passed on to the underlying lattice methods.

### Details

The function draws a scatter plot matrix of the data for each flow parameter in a `flowFrame`. For the most, one can think about this as a rectangular arrangement of separate `xyplots`, and most of that functionality is also available here. To be more precise, the function repeatedly calls `panel.xyplot.flowframe` to do the actual plotting. Please see its documentation for details.

### Methods

splom
  `signature(x = "flowFrame", data = "missing")`: Creates a scatter plot matrix for a whole `flowFrame`. The actual plotting is done by `panel.xyplot.flowframe`, so most additional arguments from the regular `xyplot` are also valid here.

### Author(s)

F. Hahne, D. Sarkar

### See Also

Not all standard lattice arguments will have the intended effect, but many should. For a fuller description of possible arguments and their effects, consult documentation on lattice.

### Examples

    data(GvHD)

    tf <- transformList(colnames(GvHD)[3:7], asinh)
    dat <- tf %on% GvHD[[3]]

    ## scatter plot matrix of individual flowFrames
    lattice.options(panel.error=NULL)
    splom(dat)

    splom(dat[,1:3], smooth = FALSE)

    ## displaying filters
    rg <- rectangleGate("FSC-H"=c(200,400), "SSC-H"=c(300,700),
    "FL1-H"=c(2,4), "FL2-A"=c(4,7))
    splom(dat, filter=rg)

    splom(dat, filter=rectangleGate("FSC-H"=c(400,800)))

    splom(dat[,1:4], smooth = FALSE, filter=norm2Filter("FSC-H", "SSC-H", scale=1.5))

[Package flowViz version 1.8.0 Index]