plot.ProbBin.FCS {rflowcyt}R Documentation

Plots a ProbBin.FCS object

Description

A ProbBin.FCS object plot results in two histograms–one for the stimulated sample and one for the unstimulated sample.

Usage

  plot.ProbBin.FCS(x, xlab=x$varname,
               xlim=c(min(c(round(range(x$st.hist$breaks),1) + 1, 
                  round(range(x$unst.hist$breaks),1) + 1)), 
                  max(c(round(range(x$st.hist$breaks),1) + 1, 
                  round(range(x$unst.hist$breaks),1) + 1))),
            
              main="", 
              labels=FALSE, 
              freq=FALSE, plots.made=c("both", "stimulated", "unstimulated"), ...)

Arguments

x ProbBin.FCS object
xlab Character string of the x-axis; default is the variable name
xlim vector of length 2 denoting the minimum and the maximum value of the breakpoint values, x-axis; default is the minimum and the maximum of the breakpoints for both stimulated and unstimulated samples
main character string of the title of the file (ie, individual id number)
labels Boolean; if TRUE, then the number/precentage in each bin is printed on the histogram, otherwise it is not; default is FALS
freq Boolean; if TRUE, then the histogram is in terms of counts; if FALSE, then the histogram is in terms of relative frequencies/precentages; if TRUE and the areas in plot are wrong is output as a warning.
plots.made character string denoting which histogram plot should be displayed; default is "both"
... plotting options such as 'ylab' and 'ylim' to pass to hist

Value

Two histograms (one of the stimulated sample, and the other of the unstimulated sample) are displayed or only one histogram plot specified by the user will be displayed.

Author(s)

A.J. Rossini & J.Y. Wan

References

Mario Roederer, et al. "Probability Binning Comparison: A Metric for Quantitating Univariate Distribution Differences" Cytometry 45:37-46 (2001).

See Also

hist, ProbBin.FCS

Examples


if (require(rfcdmin)){

if (!( is.element("st.1829", objects()) & is.element("unst.1829",
objects()) )){
## obtaining the FCS objects from VRC data
data(VRCmin)
}

## This only serves as an example.
## Gating/subsetting should precede this analysis
IFN.gamma.1<-unst.1829@data[1:2000,4]
IFN.gamma.2<-st.1829@data[1:2000,4]

#Probability binning using the control dataset to determine the breaks
PB1<-ProbBin.FCS(IFN.gamma.1, IFN.gamma.2, 200,
varname=colnames(unst.1829@data)[4], PBspec="by.control",MY.DEBUG=FALSE)

## Probability Binning using the combined dataset (control and stimulated)
## to determing the breaks
PB2<-ProbBin.FCS(IFN.gamma.1, IFN.gamma.2, 200,
varname=colnames(unst.1829@data)[4], PBspec="combined",MY.DEBUG=FALSE)

if (interactive()){
par(mfrow=c(2,2))
## plots both plots
plot(PB1, ylim=c(0,500),main="Prob Binning using the Control dataset")

## plots only the unstimulated
plot(PB2, main="Prob Binning using the Combined Dataset", plots.made="unstimulated")

## plots only the stimulated
plot(PB2, main="Prob Binning using the Combined Dataset", plots.made="stimulated")
}

}


[Package rflowcyt version 1.4.0 Index]