1/12/14

This repository contains several files that are helpful for reproducing the main figure of the Novembre et al 2008 ``Genes Mirror Geography in Europe'' paper.

The raw POPRES data must be accessed via dbGAP.

File descriptions:

==== Main files for plotting of PCA plot  ====

PCA.txt : File with basic results for plotting
        ID: The individual ID
        plabels:  Population labels
        alabels: Abbreviated label
        longitude: longitude used in study for that population
        latitude: latitude used in study for that population
        PC1: self-explanatory
        PC2: self-explanatory
        RotNS:  North/South coordinate after rotation of PCA (see methods)
        RotEW: East/west coordinate after rotation of PCA (see methods)

POPRESID_Color.txt : Color used for each individual in plot

==== Files for geographic plot ====

world_countries.rda : World polygon data
ColorTablePCmap.txt : Color used for each country in the geographic inset map

To generate the colored geographic map:

library(sp)
library(rgdal)
load("world_countries.rda")
coldatamap=read.table("ColorTablePCmap.txt",sep="\t",as.is=TRUE)
names(coldatamap)=c("cntry","color")
row.names(coldatamap)=toupper(coldatamap$cntry)
plot(worldpolys,xlim=c(-8,35),ylim=c(35,60),col=coldatamap[toupper(worldpolys$names),"color"])

===== Miscellaneous files =====

POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.bim : A .bim file in plink format describing the 197,146 markers used in the thinned dataset for the PCA analysis.

POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.fam : A .fam file in plink format describing the 1,387 individuals used in the thinned dataset for the PCA analysis.

affyProves-rsid.txt : A mapping of Affymetrix probe names to rsid's.

POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.out0-PCA.par : Input file for smartpca
POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.out0-PCA.eigs : Smartpca output with individual coordinates
POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.out0-PCA.eval : Smartpca output with eigenvalues 
POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.out0-PCA.snpeigs : Smartpca output containing SNP loadings that define the principal components