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.
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).
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(immunoClust)
Loading required package: grid
Loading required package: lattice
Loading required package: flowCore
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/immunoClust/plot.immunoClust.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.immunoClust
> ### Title: Scatterplot of immunoClust Clustering Results
> ### Aliases: plot plot.immunoClust plot,immunoClust-method
> ### plot,immunoClust,missing-method plot.immunoClust
> ### Keywords: graphs
>
> ### ** 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)
>
>
>
>
>
> dev.off()
null device
1
>