makeTernaryData: Prepare PFD Data for a Call to ternaryplot()

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

Description

This function takes a dataframe of polyfunctional degree (pfd) data and prepares a matrix with 3 columns (egs. PFD1,PFD2,PFD3, or PFD1-2, PFD3-4, PFD5-6) to use as input to ternaryplot() in the vcd pkg. If multiple columns are specified for one of the three columns, the percentages for the multiple columns will be summed.

Usage

   makeTernaryData(pfdData, columns1, columns2, columns3, 
      columnNames=c("PFD=1","PFD=2","PFD=3"))

Arguments

pfdData	data frame containing data for 1 or more groups
columns1	numeric; column(s) of pfd data to place in the first column of the matrix
columns2	numeric; column(s) of pfd data to place in the second column of the matrix
columns3	numeric; column(s) of pfd data to place in the third column of the matrix
columnNames	(optional) character vector of names for the three columns of the matrix

Value

matrix of 3 columns; rows = subjects, cols = data for each point on the triangle

Author(s)

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

See Also

StackedData

Examples

## Load the PFD Data to plot in a ternary 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 the ternary plot

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

## Prepare a legend with group stats

adultPFDData = subset(pfdDataSubset, group=="adult", select=c(PFD1:PFD3))
neoPFDData = subset(pfdDataSubset, group=="neonate", select=c(PFD1:PFD3))
groupPFDDataList = list(adultPFDData, neoPFDData)
pfdGroupStatsList = computePFDGroupStatsList(groupPFDDataList, pfdValues=1:3, numDigitsMean=3, 
   numDigitsSD=2)
groupNames = c("Adults","Neonates")
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.