plotBins: Plots the probability bins overlaid with flowFrame data

In RGLab/flowStats: Statistical methods for the analysis of flow cytometry data

Plots the probability bins overlaid with flowFrame data

Description

This function is useful in visualizing the differences between the binned control and sample datasets. The bins generated from the control dataset are overlaid with the sample dataset. An optional argument residuals can be used to shade each bin based on a calculated statistical measure of difference between the number of events in each bin.

Usage

plotBins(binRes,data,channels,title,residuals,shadeFactor)

Arguments

binRes	The result generated by calling the probBin function on a control dataset.
data	An object of class flowFrame sample(dataset)
channels	The flow parameters to be plotted.In cases where more than two parameters are binned from the control set, the plotBins function plots the projections of the hyperplanes in 2 dimensions)
title	Optional title for the plot generated
residuals	A vector of length equal to the number of bins generated that can be used to shade each bin. The residuals from the calcPearsonChi function or the calcPBChiSquare function can be used to highlight the bins that are different between control and sample datasets
shadeFactor	Optional argument between 0 and 1 that controls the intensity of the shading of bins

Author(s)

Nishant Gopalakrishnan

See Also

proBin, calcPearsonChi, calcPBChiSquare

Examples

library(flowCore)
data(GvHD)
# flow frame 1 is treated as  control dataset and used to generate bins
resCtrl<-proBin(GvHD[[1]],200,channels=c("FSC-H","SSC-H"))
plotBins(resCtrl,GvHD[[1]],channels=c("FSC-H","SSC-H"),title="Binned control data")
# Same bins are applied to flowFrame 16
resSample<-binByRef(resCtrl,GvHD[[16]])
stat<-calcPearsonChi(resCtrl,resSample)
dev.new()
plotBins(resCtrl,data=GvHD[[16]],channels=c("FSC-H","SSC-H","Time"),title="Comparision 1 & 16",
residuals=stat$residuals[2,],shadeFactor=0.7)

RGLab/flowStats documentation built on July 20, 2023, 1:33 a.m.