Add a pedigree tree/diagrams to the example def-file explanations

[nh13]

I had to draw them out to visualize the example relationships. It would be great to include a image per def in the examples to verify.

[nh13]

Here's a really ugly script to plot the .fam file adapted from here

require(kinship2)

args<-commandArgs(TRUE)
pedPath<-args[1]
pdfFile<-args[2]

pedfile <- read.table(pedPath,sep=" ")
pedfile$V5 <- apply(pedfile,1,function(data){if(data[5] == 1 || data[5] ==2){data[5]}else{3}}) 
pedfile$affected <- apply(pedfile,1,function(data){if(as.numeric(data[6]) == 1){res <- data[6]}else{if(as.numeric(data[6]) == 2){res <- data[6]}else{res <-0}}})

familyIDs <- as.character(unique(pedfile$V1))

pdf(file=pdfFile, width=12, height=12)
for(famID in familyIDs){
    ped <- pedigree(id=as.character(pedfile$V2[pedfile$V1==famID]),dadid=as.character(pedfile$V3[pedfile$V1==famID]),momid=as.character(pedfile$V4[pedfile$V1==famID]),sex=as.numeric(pedfile$V5[pedfile$V1==famID]),affected=as.numeric(pedfile$affected[pedfile$V1==famID]))
    plot.pedigree(ped,cex=0.7,align=TRUE)
    title(famID)
}

[williamslab]

Though simple, plot-fam.R plots all the families in a fam file (see this section in the README).