Simulation code, simulated data sets, and analysis for A Genealogical Look at Shared Ancestry on the X Chromosome

This repository contains the code and other materials for our paper *A Genealogical Look at Shared Ancestry on the X Chromosome. A preprint of our manuscript is available on bioRxiv.

Contents

• Makefile: main makefile for the repository; runs simulations to generate data, runs analysis for plots.

• data/: directory containing simulated datasets used in the paper.

• ancestrysim/: directory containing genealogical simulation code. This includes the prototype Python routine ancestralsim.py and the finalized C/Python ancestrysim2.py version.

• paper/: empty directory which was home to the manuscript, now contains paper/images which contains images produced by plots.R.

• plots.R: R code to run analyses and generate paper's figures.

• dist-functions.R: distribution functions, test code, and other functions used by plots.R.

• jsviz/: code for visualizations made with Javascript/d3 for paper.

• images/: other images and image requisites like .dot files.

Session Info

Here's the sessionInfo() from R, after plots.R was run:

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin14.5.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] colorspace_1.2-6   RColorBrewer_1.1-2 readr_0.2.2        tidyr_0.4.0
 [5] wesanderson_0.3.2  reshape2_1.4.1     purrr_0.2.0        dplyr_0.4.3
 [9] scales_0.3.0       ggplot2_2.0.0      devtools_1.9.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2     digest_0.6.9    assertthat_0.1  plyr_1.8.3
 [5] R6_2.1.1        gtable_0.1.2    DBI_0.3.1       magrittr_1.5
 [9] stringi_1.0-1   lazyeval_0.1.10 tools_3.2.2     stringr_1.0.0
[13] munsell_0.4.2   parallel_3.2.2  memoise_0.2.1k