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

In gap: Genetic Analysis Package

Converting pedigree(s) to dot file(s)

Description

Converting pedigree(s) to dot file(s)

Usage

pedtodot(
  pedfile,
  makeped = FALSE,
  sink = TRUE,
  page = "B5",
  url = "https://jinghuazhao.github.io/",
  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.

Details

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.

Note that a single PostScript (PDF) file can be obtainaed by dot, fdp, or neato.

dot -Tps <dot file> -o <ps file>

or

fdp -Tps <dot file> -o <ps file>

or

neato -Tps <dot file> -o <ps file>

See relevant documentations for other formats.

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 <ps file>

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

Under Linux, you can also visualize the .dot file directly via command,

dotty <dot file> &

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

sh pedtodot <pedigree file>

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.

Note

This is based on the gawk script program pedtodot by David Duffy with minor changes.

Author(s)

David Duffy, Jing Hua Zhao

See Also

package sem in CRAN and Rgraphviz in BioConductor https://www.bioconductor.org/.

Examples

## Not run: 
# 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="https://jinghuazhao.github.io/")

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

## End(Not run)

gap documentation built on Sept. 11, 2024, 5:36 p.m.