computePFDGroupStatsList: Compute Group Stats on PFD Data to Be Used In a Legend

In flowPlots: flowPlots: analysis plots and data class for gated flow cytometry data

Description

This function can be used with ternaryplot() to add PFD group stats to, say, the legend. The stats computed are group size (N), pfd group mean, and pfd group standard deviation.

Usage

   computePFDGroupStatsList(groupPFDDataList, pfdValues=1:3, numDigitsMean=3, numDigitsSD=2)    

Arguments

groupPFDDataList	one list item per group, each list item contains a matrix of PFD percentages; the rows are subjects, and the columns are pfd categories.
pfdValues	vector of the PFD values that the columns in each matrix in the groupPFDDataList represent; eg. 1:3 for (PFD1,PFD2,PFD3).
numDigitsMean	return a mean rounded to this number of digits
numDigitsSD	return a standard deviation rounded to this number of digits

Value

a list; each list item contains the stats for a group as a 3 element character vector containing the size of the group, the mean PFD, and the standard deviation of the PFD.

Author(s)

N. Hawkins, Fred Hutchinson Cancer Research Center, Seattle, WA

See Also

StackedData, pfdData

Examples

## Load PFD data to plot
data(pfdDF)
pfdDataSubset = subset(pfdDF, stim=="LPS" & concGroup==3 & cell=="mDC")

## Prepare the PFD Data for a call to ternaryplot()
ternaryData = makeTernaryData(pfdDataSubset, 1, 2, 3:4)
colnames(ternaryData) = c("PFD1", "PFD2", "PFD3-4")

## Make a ternary plot
library(vcd)
ternaryplot(ternaryData, cex=.5, col=as.numeric(pfdDataSubset$group)*2, main="Stimulation = LPS, 
   Concentration Group = 3, Cell = mDC")

## Compute Group Stats to use in the legend of the ternary plot
adultPFDData = subset(pfdDataSubset, group=="adult", select=c(PFD1:PFD3))
neoPFDData = subset(pfdDataSubset, group=="neonate", select=c(PFD1:PFD3))
groupPFDDataList = list(adultPFDData, neoPFDData)

## Specifically, compute the PFD Group Stats List
pfdGroupStatsList = computePFDGroupStatsList(groupPFDDataList, pfdValues=1:3, numDigitsMean=3, 
   numDigitsSD=2)
groupNames = c("Adults","Neonates")

## Create group names for the legend based on the PFD Group Stats List
legendNames = legendPFDStatsGroupNames(pfdGroupStatsList,groupNames)
grid_legend(0.8, 0.7, pch=c(20,20), col=c(2,4), legendNames, title = "Group (n), mean/sd:", 
   gp=gpar(cex=.8))

flowPlots documentation built on Nov. 8, 2020, 7:54 p.m.