R Markdown scripts for spatial PCA (sPCA) analysis of genotype data
This set of scripts specifies csv files for genotypes and population data (including latitude/longitude of all samples) for spatial PCA analysis (see Jombart, T., Devillard, S., Dufour, A.B., Pontier, D., 2008. Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity (Edinb) 101, 92-103), and conducts global, local, and Monte Carlo randomization tests (Monte Carlo test for presence of significant spatial structure in sPCA: Montano and Jombart BMC Bioinformatics (2017) 18:562, DOI 10.1186/s12859-017-1988-y (https://github.com/thibautjombart/adegenet/blob/master/R/spca_randtest.R)). Summary files and figures can be output as .csv and pdf files (pdf output has been commented out in most sections in this version)