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.

Usage

pedtodot(
  pedfile,
  makeped = FALSE,
  sink = TRUE,
  page = "B5",
  url = "https://jinghuazhao.github.io/",
  height = 0.5,
  width = 0.75,
  rotate = 0,
  dir = "none"
)

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.

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.

Author

David Duffy, Jing Hua Zhao

Details

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

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

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

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: