library("ggplot2") library("Rmisc") library("qqman") library("devtools") library("ggrepel") library("ggman") library("cowplot") library("magrittr") library("reshape") library("plyr") library("lattice") # Fst --------------------------------------------------------------------- # Genome wide Fst --------------------------------------------------------- ### Plot Locus Fst across the genome ### Locus_Fst_CAN <- read.table("Berthelots_Canaries_subset_maf_trim_0.03_Plinkrel0.2.fst", header = T,stringsAsFactors = F) Locus_Fst_MAD <- read.table("Berthelots_Madeira_subset_maf_trim_0.03_Plinkrel0.2.fst", header = T,stringsAsFactors = F) Locus_Fst_MAD_mapped <- subset(Locus_Fst_MAD, CHR >0) Locus_Fst_CAN_mapped <- subset(Locus_Fst_CAN, CHR >0) # Eigenvecotor PCA -------------------------------------------------------- egvec_CAN <- read.table("Berthelots_Canaries_subset_maf_trim_0.03_Plinkrel0.2.eigenvec") egvec_MAD <- read.table("Berthelots_Madeira_subset_maf_trim_0.03_Plinkrel0.2.eigenvec") # Eigenvalues Manhatton Plot ---------------------------------------------- eg1_CAN <- read.table("Berthelots_Canaries_subset_maf_trim_0.03_Plinkrel0.2.1.egwas", header = T,stringsAsFactors = F) eg2_CAN <- read.table("Berthelots_Canaries_subset_maf_trim_0.03_Plinkrel0.2.2.egwas", header = T,stringsAsFactors = F) eg1_MAD <- read.table("Berthelots_Madeira_subset_maf_trim_0.03_Plinkrel0.2.1.egwas", header = T, stringsAsFactors = F) eg2_MAD <- read.table("Berthelots_Madeira_subset_maf_trim_0.03_Plinkrel0.2.2.egwas", header = T, stringsAsFactors = F)