Is there a pedigree viewer that works with PLINK pedigree files? I saw an old post by Pierre, but I don't see the script on his blog.
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1$\begingroup$ We use R package kinship2 here: cran.r-project.org/web/packages/kinship2/index.html $\endgroup$– Eric C.Commented Aug 17, 2018 at 10:04
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We use kinship2 R package to visualize pedigree files (.fam plink files). For some reasons, some characters from plink ped aren't supported (like "-9" for unknown genre or affected status).
Here is the R script we use:
args<-commandArgs(TRUE)
pedPath<-args[1]
pdfFile<-args[2]
library(kinship2)
pedfile <- read.table(pedPath,sep="\t")
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 <- NA}}})
familyIDs <- as.character(unique(pedfile$V1))
pdf(file=pdfFile)
for(famID in familyIDs){
ped <- pedigree(id=as.character(pedfile$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$V1==famID]))
plot.pedigree(ped,cex=0.7,align=TRUE)
title(famID)
}
And we call it this way:
Rscript <kinshipScript.R> <plink ped file> <pdf output>
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$\begingroup$ Now, if only I could convince people to include affected information in the actual .fam files. :-) $\endgroup$ Commented Aug 18, 2018 at 14:15
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$\begingroup$ @MarkEbbert affected status is not really necessary but it still looks good on the pdf :) $\endgroup$– Eric C.Commented Aug 20, 2018 at 9:38