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") } }