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#load in acerifolia data
setwd("../../Data_Files/Adegenet_Files")
QUAC_gen <- read.genepop("QUAC_allpop_clean.gen")
library(adegenet)
..
setwd("..")
QUAC_gen <- read.genepop("Adegenet_Files/QUAC_allpop_clean.gen")
QUAC_gen <- read.genepop("Adegenet_Files/QUAC_allpop_clean.gen", ncode = 3)
QUAC_df <- read.csv("Data_Frames/QUAC_clean_df.csv")
table(QUAC_gen@pop)
#load in acerifolia data
setwd("C:\\Users\\eschumacher\\Documents\\GitHub\\GCC_QUAC_ZAIN")
table(QUAC_gen@pop)
levels(QUAC_gen@pop) <- c("Garden", "Wild")
QUAC_gen <- read.genepop("Adegenet_Files/Garden_Wild/QUAC_allpop_clean.gen", ncode = 3)
QUAC_gen <- read.genepop("Data_Files/Adegenet_Files/Garden_Wild/QUAC_allpop_clean.gen", ncode = 3)
QUAC_gen <- read.genepop("Data_Files/Adegenet_Files/Garden_Wild/QUAC_woK_garden_wild_clean.gen", ncode = 3)
levels(QUAC_gen@pop) <- c("Garden", "Wild")
View(QUAC_df)
rownames(QUAC_gen@tab) <- QUAC_df[,1]
length(rownames(QUAC_gen@tab))
QUAC_df <- read.csv("Data_Files/Data_Frames/QUAC_woK_garden_allwildpop_df.csv")
QUAC_df <- read.csv("Data_Files/Data_Frames/Garden_Wild/QUAC_woK_garden_allwildpop_df.csv")
rownames(QUAC_gen@tab) <- QUAC_df[,1]
?find.cluster
?find.clusters
find.clusters(QUAC_gen)
?compoplot
tab(QUAC_gen)
?dapc
find.clusters(QUAC_gen)
QUAC_cluster <- find.clusters(QUAC_gen)
QUAC_dapc <- dapc(QUAC_cluster)
QUAC_dapc <- dapc(QUAC_cluster$grp)
QUAC_cluster
QUAC_cluster$stat
QUAC_cluster$size
QUAC_cluster$grp
QUAC_cluster$stat
QUAC_cluster$size
QUAC_dapc <- dapc(QUAC_gen, pop = QUAC_cluster$grp)
compoplot(QUAC_dapc)
find.clusters(QUAC_gen)
QUAC_dapc <- dapc(QUAC_gen, pop = QUAC_cluster$grp)
compoplot(QUAC_dapc)
QUAC_cluster <- find.clusters(QUAC_gen)
QUAC_cluster$grp
levels(QUAC_cluster$grp)
QUAC_gen
QUAC_dapc <- dapc(QUAC_gen, pop = QUAC_cluster$grp)
compoplot(QUAC_dapc)
#load in acerifolia data
setwd("C:/Users/eschumacher/Documents/GitHub/GCC_QUAC_ZAIN")
QUAC_dapc
dev.off()
compoplot(QUAC_dapc)
pdf("G:/Shared drives/Emily_Schumacher/Project_Folders/GCC_QUAC_ZAIN/Analyses/Results/Clustering/QUAC_dapc.pdf", width = 20, height = 10)
compoplot(QUAC_dapc)
dev.off()