plot.immunoClust {immunoClust} | R Documentation

## Scatterplot of immunoClust Clustering Results

### Description

This method generates scatterplot revealing the cluster assignment.

### Usage

    ## S4 method for signature 'immunoClust'
    plot(x, data, subset=c(1,2), ellipse=T,
    show.rm=F, include=1:(x@K), main=NULL,
    col=include+1, pch=".", cex=0.6,
    col.rm=1, pch.rm=1, cex.rm=0.6, ecol=col, elty=1,
    npoints=501, add=F, ...)

### Arguments

`x` | An object of class `immunoClust` as return by `cell.process`.
`data` | A matrix, data frame of observations, or object of class `flowFrame`. This is the object of observations on which `cell.process` was performed or the matrix of cell-cluster centers for the `meta.process`.
`subset` | A numeric vector of length two indicating which two parameters are selected for the scatterplot. Alternatively, a character vector containing the names of the two parameters is allowed if `x@parameters` is not `NULL`.
`ellipse` | A logical value indicating whether the cluster 90% percentil boundary is to be drawn or not.
`show.rm` | A logical value indicating whether filtered observations will be shown or not.
`include` | A numeric vector specifying which clusters will be shown on the plot. By default, all clusters are included.
`main` | Title of the plot.
`col` | Color(s) of the plotting points. May specify a different color for each cluster.
`pch` | Plotting character(s) of the plotting points. May specify a different character for each cluster.
`cex` | Size of the plotting characters. May specify a different size for each cluster.
`col.rm` | Color of the plotting characters denoting filtered observations.
`pch.rm` | Plotting character used to denote filtered observations.
`cex.rm` | Size of the plotting character used to denote filtered observations.
`ecol` | Color(s) of the lines representing the cluster boundaries. May specify a different color for each cluster.
`elty` | Line type(s) drawing the cluster boundaries. May specify a different line type for each cluster.
`npoints` | The number of points used to draw each cluster boundary.
`add` | A logical value. If `TRUE`, add to the current plot.
`...` | Further graphical parameters passed to the generic function `plot`.

### Value

Plots the clustering assignment on an appropriatei plotting device.

### Author(s)

Till Sörensen till-antoni.soerensen@charite.de

### References

Sörensen, T., Baumgart, S., Durek, P., Grützkau, A. and Häupl, T. immunoClust - an automated analysis pipeline for the identification of immunophenotypic signatures in high-dimensional cytometric datasets. Cytometry A (accepted).

### See Also

`immunoClust-object`

### Examples

    data(dat.fcs)
    data(dat.exp)
    dat.res <- dat.exp[[1]]
    dat.trans <- trans.ApplyToData(dat.res, dat.fcs)
    plot(dat.res, dat=dat.trans)

[Package immunoClust version 1.18.1 Index]