plot.immunoClust: Scatterplot of immunoClust Clustering Results

In immunoClust: immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

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 [e-mail]

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)

immunoClust documentation built on Nov. 8, 2020, 5:19 p.m.