| plot.ProbBin.FCS {rflowcyt} | R Documentation |
A ProbBin.FCS object plot results in two histograms–one for the stimulated sample and one for the unstimulated sample.
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"), ...)
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 |
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.
A.J. Rossini & J.Y. Wan
Mario Roederer, et al. "Probability Binning Comparison: A Metric for Quantitating Univariate Distribution Differences" Cytometry 45:37-46 (2001).
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")
}
}