README.md

pedvis

A tiny package to take a data frame that lists a pedigree in three columns (kid, pa, ma) and make a .dot file for a marriage node diagram of the thing. It also will write it out as a factor graph. And it will run dot on it if you have dot in your system path.

This is sort of a hairball at the moment, and I would do it all differently if I had the time to do it over, but oh well. it works for what I want to do at the moment.

The documentation isn't complete, but I mostly want to get this thing up on GitHub so Clemento, my homie at the lab, can draw some pedigrees.

Preliminaries

  1. You should have dot from the Graphviz package installed. If not, get it from http://www.graphviz.org/ for your system and install it and make sure that dot is in your PATH.

  2. You should have epstodpdf on your system. i.e. you ought to have ImageMagick or something of the sort.

  3. The program will try to open a PDF file with a system call to the "open" command, which might be a Mac thing, and not portable.

Getting the package and some examples.

The easiest way to get and install this package is with the devtools package from within R:

devtools::install_github("pedvis", "eriqande")

Then, if that was successful, here you can see what the input is all about and do some examples

library(pedvis)  # load the package

# here is a simple input pedigree
simple_test_ped()

Note that the names of the individuals have to be strings NOT factors or integers. So, use stringsAsFactors = FALSE if reading in a data frame with read.table.

Here we draw that simple pedigree as a marriage node diagram and we put labels on everyone and we make some of the p-node factors invisible (that should sound cryptic...). And we make a few of the individuals shaded by telling the function we have observed data on them.

stp <- simple_test_ped()
all_names <- unique(unlist(stp))
out_list <- ped2dot(stp, 
                    ShowLabelNodes = all_names, 
                    pfactorNodeStyle = "invis", 
                    pfactorEdgeStyle = "invis", 
                    ObsNodes = c(letters[1:8], 1:5, 10:12), 
                    outf = "testy"
                    )

Note that running this function will create a file called testy.dot in the current working directory. It will then run dot on it and make testy.ps, and then convert that to a pdf with epstopdf. Then it will open that PDF file with the default PDF viewer. It also makes an svg version so you can edit it with Inkscape.



eriqande/pedvis documentation built on May 13, 2017, 8:22 p.m.