plot.immunoClust {immunoClust} | R Documentation |
This method generates scatterplot revealing the cluster assignment.
## 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, ...)
x |
An object of class |
data |
A matrix, data frame of observations, or object of class
|
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 |
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 |
... |
Further graphical parameters passed to the generic function
|
Plots the clustering assignment on an appropriatei plotting device.
Till Sörensen till-antoni.soerensen@charite.de
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).
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)