pedtodot: Converting pedigree(s) to dot file(s)

Description

This function converts GAS or LINKAGE formatted pedigree(s) into .dot file for each pedigree to be used by dot in graphviz, which is a flexible package for graphics freely available from http://www.graphviz.org

Note that a single PostScript file is obtainable by specifyiing *.dot to dot or neato.

dot -Tps -o

neato -Tps -o

However, to preserve the original order of pedigree(s) in the data, you can examine the examples at the end of this document.

Under Cygwin/Linux/Unix, the PostScript file can be converted to Portable Document Format (PDF) default to Acrobat.

ps2pdf

Use ps2pdf12, ps2pdf13, or ps2pdf14 for appropriate versions of Acrobat according to information given on the headline of .

Usage

pedtodot(pedfile,makeped=FALSE,sink=TRUE,page="B5",
         url="http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/r-progs.htm",
         height=0.5,width=0.75,rotate=0,dir="none")

Arguments

pedfile

a pedigree file in GAS or LINKAGE format, note if individual's ID is character then it is necessary to specify as.is=T in the read.table command

makeped

a logical variable indicating if the pedigree file is post-makeped

sink

a logical variable indicating if .dot file(s) are created

page

a string indicating the page size, e.g, A4, A5, B5, Legal, Letter, Executive, "x,y", where x, y is the customized page size

url

Unified Resource Locator (URL) associated with the diagram(s)

height

the height of node(s)

width

the width of node(s)

rotate

if set to 90, the diagram is in landscape

dir

direction of edges, i.e., "none", "forward","back","both". This will be useful if the diagram is viewed by lneato

Value

For each pedigree, the function generates a .dot file to be used by dot. The collection of all pedigrees (*.dot) can also be put together.

Details

We can extract the code below (or within pedtodot.Rd) to pedtodot and then use command:

sh pedtodot

# Read a GAS or LINKAGE format pedigree, return a digraph in the dot language # call dot to make pedigree drawing # AWK=/bin/gawk DOTEXE=/usr/local/bin/dot # cygwin # AWK=/bin/gawk # DOTEXE=c:/local/graphviz/bin/dot

for fil in $* do for ped in `$AWK '!/^[!#]/ {print $1}' $fil | sort -u` do echo "Pedigree $ped" $AWK -v ped=$ped ' BEGIN { shape["m"]="box,regular=1" shape["1"]="box,regular=1" shape["f"]="circle" shape["2"]="circle" shade["y"]="blue" shade["2"]="blue" shade["n"]="grey" shade["1"]="grey" shade["x"]="green" shade["0"]="green" } !/^[!#]/ && $1==ped { sex[$2]=$5 aff[$2]="x" ; if ($6 ~ /[012nyx]/) aff[$2]=$6 if($3!="x" && $3!="0") { marriage[$3,$4]++ child[$3,$4,marriage[$3,$4]]=$2 } } END { print "digraph Ped_" ped " {" print "# page =\"8.2677165,11.692913\" ;" print "ratio =\"auto\" ;" print "mincross = 2.0 ;" print "label=\"Pedigree " ped "\" ;" print "rotate=90 ;" for(s in sex) { print "\"" s "\" [shape=" shape[sex[s]] "," \ " style=filled,color=" shade[aff[s]] "] ;" } for(m in marriage) { n=split(m,par,"\034") mating="\"" par[1] "x" par[2] "\"" print mating "[shape=diamond,style=filled," \ "label=\"\",height=.1,width=.1] ;" print "\"" par[1] "\" -> " mating " [dir=none, weight=1] ;" print "\"" par[2] "\" -> " mating " [dir=none, weight=1] ;" for(k=1;k<=marriage[par[1],par[2]];k++) {="" print="" mating="" "="" -=""> \"" child[par[1],par[2],k] "\"" \ " [dir=none, weight=2] ;" } } print "}" }' $fil > $ped.dot $DOTEXE -Tps $ped.dot -o $ped.ps done done $DOTEXE -Tps *.dot -o $*.ps

Examples

Run this code

# example as in R News and Bioinformatics (see also plot.pedigree in package kinship)
# it works from screen paste only
p1 <- scan(nlines=16,what=list(0,0,0,0,0,"",""))
 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 

p2 <- as.data.frame(p1)
names(p2) <-c("id","fid","mid","sex","aff","GABRB1","D4S1645")
p3 <- data.frame(pid=10081,p2)
attach(p3)
pedtodot(p3)
#
# Three examples of pedigree-drawing
# assuming pre-MakePed LINKAGE file in which IDs are characters
pre<-read.table("pheno.pre",as.is=TRUE)[,1:6]
pedtodot(pre)
dir()      
# for post-MakePed LINKAGE file in which IDs are integers
ped <-read.table("pheno.ped")[,1:10]
pedtodot(ped,makeped=TRUE)
dir()
# for a single file with a list of pedigrees ordered data
sink("gaw14.dot")
pedtodot(ped,sink=FALSE)
sink()
file.show("gaw14.dot")
# more details
pedtodot(ped,sink=FALSE,page="B5",url="http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/r-progs.htm")

# An example from Richard Mott and in the demo
filespec <- file.path(.path.package("gap"),"tests/ped.1.3.pre")
pre <- read.table(filespec,as.is=TRUE)
pre
pedtodot(pre,dir="forward")