Overview

This document is to highlight some of the capabilities using R for plotting pedigree data.

The ‘kinship2’ Package

This package has some sample pedigree data. We will use that to take a quick look of pedigree plotting using R.

Load a sample pedigree dataset

library(kinship2)

## Loading required package: Matrix
## Loading required package: quadprog

data(sample.ped)

This following code loads 5 data fields:

Person ID
Father ID
Mother ID
Person gender
Person Family ID

pedAll <- pedigree(
        id=sample.ped$id, 
        dadid=sample.ped$father, 
        momid=sample.ped$mother,
        sex=sample.ped$sex, 
        famid=sample.ped$ped)
print(pedAll)

## Pedigree list with 55 total subjects in 2 families

Noticed that we have not touched any disease states in this plot.

Plot first family

This first plot is for family 1.

ped1basic <- pedAll['1']
plot(ped1basic, main = "First Family")

## Did not plot the following people: 113

Plot second family

This second plot is for family 2.

ped2basic <- pedAll['2']
plot(ped2basic, main = "Second Fammily")

Demo Affected Indicators with Relationships

We will add additional details to the plot, we will add the following:

show affected status (for disease state)
show 210 and 211 are monozygotic twins (must be of same gender)
show 212 and 213 are dizygotic twins.

Some of the relationship codes are:

Monozygotic twin
Dizygotic twin
Twin of unknown zygosity
Spouse

sample.ped2 = subset(sample.ped, ped == 2)
id1 = c(210, 212)
id2 = c(211, 213)
r = c(1, 2)
rm = cbind(id1, id2, r)

pedAll <- pedigree(
    id = sample.ped2$id, 
    dadid = sample.ped2$father, 
    momid = sample.ped2$mother, 
    sex = sample.ped2$sex, 
    affected = sample.ped2$affected, 
    status = sample.ped2$status, 
    relation = rm)
plot(pedAll, main = "Twins: 210-211, 212-213")

Demo Genotype Annotation

The following sample is based on this Pedigree-drawing with R and graphviz article.

First, create a CSV file

Here is a quick look of the data file.

cat test.pre

## "id" "fid"   "mid"   "sex"   "aff"   "GABRB1"    "D4S1645"
## 1    2   3   2   2   7/7 7/10    
## 2    0   0   1   1   -/- -/- 
## 3    0   0   2   2   7/9 3/10    
## 4    2   3   2   2   7/9 3/7 
## 5    2   3   2   1   7/7 7/10    
## 6    2   3   1   1   7/7 7/10    
## 7    2   3   2   1   7/7 7/10    
## 8    0   0   1   1   -/- -/- 
## 9    8   4   1   1   7/9 3/10    
## 10   0   0   2   1   -/- -/- 
## 11   2   10  2   1   7/7 7/7 
## 12   2   10  2   2   6/7 7/7 
## 13   0   0   1   1   -/- -/- 
## 14   13  11  1   1   7/8 7/8 
## 15   0   0   1   1   -/- -/- 
## 16   15  12  2   1   6/6 7/7

Load CSV file then plot the pedigree tree

noticed that the affected persons are showing with filled circles.
Also each person is annotated with genotype from GABARB1 and D4S1645 genes.

p1 <- read.table("test.pre", header=T)
p2 <- as.data.frame(p1)
attach(p2)
ped <- pedigree(id,fid,mid,sex,aff)
par(xpd = TRUE)
strid<-paste(id, GABRB1, D4S1645, sep="\n")
plot(ped,id=strid)

Pedigree Demo using R Packages

David Liu

November 18, 2015