R/Summarize.FST.Results.SelectionMSC.R

In radamsRHA/Misc.Statistics.Genetics.Models:

	print("please cite the following when using these functions: Adams, R.H., Schield, D.R., Card, D.C., Corbin, A., Castoe, T.A., 2017. ThetaMater: Bayesian estimation of population size parameter h from genomic data. Bioinformatics 34, 1072–1073.")


#N_1_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/N_1_E_1_AB.txt')
#N_2_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/N_2_E_1_AB.txt')
#N_3_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/N_3_E_1_AB.txt')
#N_4_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/N_4_E_1_AB.txt')
#N_5_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/N_5_E_1_AB.txt')
#N_6_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/N_6_E_1_AB.txt')
#N_7_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/N_7_E_1_AB.txt')
#N_8_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/N_8_E_1_AB.txt')
#N_9_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/N_9_E_1_AB.txt')
#S_1_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_1_E_1_AB.txt')
#S_1_E_2.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_1_E_2_AB.txt')
#S_1_E_3.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_1_E_3_AB.txt')
#S_2_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_2_E_1_AB.txt')
#S_2_E_2.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_2_E_2_AB.txt')
#S_2_E_3.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_2_E_3_AB.txt')
#S_3_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_3_E_1_AB.txt')
#S_3_E_2.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_3_E_2_AB.txt')
#S_3_E_3.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_3_E_3_AB.txt')
#S_4_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_4_E_1_AB.txt')
#S_4_E_2.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_4_E_2_AB.txt')
#S_4_E_3.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_4_E_3_AB.txt')
#S_5_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_5_E_1_AB.txt')
#S_5_E_2.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_5_E_2_AB.txt')
#S_5_E_3.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_5_E_3_AB.txt')
#S_6_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_6_E_1_AB.txt')
#S_6_E_2.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_6_E_2_AB.txt')
#S_6_E_3.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_6_E_3_AB.txt')
#S_7_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_7_E_1_AB.txt')
#S_7_E_2.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_7_E_2_AB.txt')
#S_7_E_3.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_7_E_3_AB.txt')
#S_8_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_8_E_1_AB.txt')
#S_8_E_2.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_8_E_2_AB.txt')
#S_8_E_3.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_8_E_3_AB.txt')
#S_9_E_1.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_9_E_1_AB.txt')
#S_9_E_2.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_9_E_2_AB.txt')
#S_9_E_3.FST_AB.handle <- read.table(file= '~/Desktop/FST_E_AB_Results_June17/S_9_E_3_AB.txt')
#
#######################################
#N_1_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/N_1_E_1_BC.txt')
#N_2_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/N_2_E_1_BC.txt')
#N_3_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/N_3_E_1_BC.txt')
#N_4_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/N_4_E_1_BC.txt')
#N_5_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/N_5_E_1_BC.txt')
#N_6_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/N_6_E_1_BC.txt')
#N_7_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/N_7_E_1_BC.txt')
#N_8_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/N_8_E_1_BC.txt')
#N_9_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/N_9_E_1_BC.txt')
#S_1_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_1_E_1_BC.txt')
#S_1_E_2.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_1_E_2_BC.txt')
#S_1_E_3.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_1_E_3_BC.txt')
#S_2_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_2_E_1_BC.txt')
#S_2_E_2.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_2_E_2_BC.txt')
#S_2_E_3.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_2_E_3_BC.txt')
#S_3_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_3_E_1_BC.txt')
#S_3_E_2.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_3_E_2_BC.txt')
#S_3_E_3.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_3_E_3_BC.txt')
#S_4_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_4_E_1_BC.txt')
#S_4_E_2.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_4_E_2_BC.txt')
#S_4_E_3.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_4_E_3_BC.txt')
#S_5_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_5_E_1_BC.txt')
#S_5_E_2.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_5_E_2_BC.txt')
#S_5_E_3.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_5_E_3_BC.txt')
#S_6_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_6_E_1_BC.txt')
#S_6_E_2.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_6_E_2_BC.txt')
#S_6_E_3.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_6_E_3_BC.txt')
#S_7_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_7_E_1_BC.txt')
#S_7_E_2.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_7_E_2_BC.txt')
#S_7_E_3.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_7_E_3_BC.txt')
#S_8_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_8_E_1_BC.txt')
#S_8_E_2.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_8_E_2_BC.txt')
#S_8_E_3.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_8_E_3_BC.txt')
#S_9_E_1.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_9_E_1_BC.txt')
#S_9_E_2.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_9_E_2_BC.txt')
#S_9_E_3.FST_BC.handle <- read.table(file= '~/Desktop/FST_E_BC_Results_June17/S_9_E_3_BC.txt')
#
#######################################
#
#
#
#
#
#
#
#FST_AB.vec <- c(N_1_E_1.FST_AB.handle[,1],S_1_E_1.FST_AB.handle[,1],S_1_E_2.FST_AB.handle[,1],S_1_E_3.FST_AB.handle[,1],N_2_E_1.FST_AB.handle[,1],S_2_E_1.FST_AB.handle[,1],S_2_E_2.FST_AB.handle[,1],S_2_E_3.FST_AB.handle[,1],N_3_E_1.FST_AB.handle[,1],S_3_E_1.FST_AB.handle[,1],S_3_E_2.FST_AB.handle[,1],S_3_E_3.FST_AB.handle[,1])
#selection.strength = rep(c(rep("01N", 10000),rep("02WS", 10000), rep("03S", 10000), rep("03VS", 10000)), 3)
#species.depth <- rep("shallow", 120000)
#species.height <- c(rep("01recent", 40000), rep("02medium", 40000), rep("03ancient", 40000))
#treatment <-c(rep("01N_1_E_1", 10000),rep("02S_1_E_1", 10000),rep("03S_1_E_2", 10000),rep("04S_1_E_3", 10000),rep("05N_2_E_1", 10000),rep("06S_2_E_1", 10000),rep("07S_2_E_2", 10000),rep("08S_2_E_3", 10000),rep("09N_3_E_1", 10000),rep("10S_3_E_1", 10000),rep("11S_3_E_2", 10000),rep("12S_3_E_3", 10000))
#FST_AB.df <- data.frame(treatment=treatment, selection.strength =selection.strength, species.depth=species.depth, species.height=species.height, FST_AB.vec=FST_AB.vec)
#
#
#
#ggplot(FST_AB.df, aes(factor(species.height), FST_AB.vec, fill=selection.strength, alpha=selection.strength)) + 
#	stat_boxplot(geom ='errorbar') + geom_boxplot()+theme_bw()+ theme(legend.position="none")
#
#########################
#
#
#FST_AB.vec <- c(N_4_E_1.FST_AB.handle[,1],S_4_E_1.FST_AB.handle[,1],S_4_E_2.FST_AB.handle[,1],S_4_E_3.FST_AB.handle[,1],N_5_E_1.FST_AB.handle[,1],S_5_E_1.FST_AB.handle[,1],S_5_E_2.FST_AB.handle[,1],S_5_E_3.FST_AB.handle[,1],N_6_E_1.FST_AB.handle[,1],S_6_E_1.FST_AB.handle[,1],S_6_E_2.FST_AB.handle[,1],S_6_E_3.FST_AB.handle[,1])
#selection.strength = rep(c(rep("01N", 10000),rep("02WS", 10000), rep("03S", 10000), rep("03VS", 10000)), 3)
#species.depth <- rep("moderate", 120000)
#species.height <- c(rep("01recent", 40000), rep("02medium", 40000), rep("03ancient", 40000))
#treatment <-c(rep("01N_1_E_1", 10000),rep("02S_1_E_1", 10000),rep("03S_1_E_2", 10000),rep("04S_1_E_3", 10000),rep("05N_2_E_1", 10000),rep("06S_2_E_1", 10000),rep("07S_2_E_2", 10000),rep("08S_2_E_3", 10000),rep("09N_3_E_1", 10000),rep("10S_3_E_1", 10000),rep("11S_3_E_2", 10000),rep("12S_3_E_3", 10000))
#FST_AB.df <- data.frame(treatment=treatment, selection.strength =selection.strength, species.depth=species.depth, species.height=species.height, FST_AB.vec=FST_AB.vec)
#
#
#
#ggplot(FST_AB.df, aes(factor(species.height), FST_AB.vec, fill=selection.strength, alpha=selection.strength)) + 
#	stat_boxplot(geom ='errorbar') + geom_boxplot()+theme_bw()+ theme(legend.position="none")
#
#
####################
#
#
#FST_AB.vec <- c(N_7_E_1.FST_AB.handle[,1],S_7_E_1.FST_AB.handle[,1],S_7_E_2.FST_AB.handle[,1],S_7_E_3.FST_AB.handle[,1],N_8_E_1.FST_AB.handle[,1],S_8_E_1.FST_AB.handle[,1],S_8_E_2.FST_AB.handle[,1],S_8_E_3.FST_AB.handle[,1],N_9_E_1.FST_AB.handle[,1],S_9_E_1.FST_AB.handle[,1],S_9_E_2.FST_AB.handle[,1],S_9_E_3.FST_AB.handle[,1])
#
#selection.strength = rep(c(rep("01N", 10000),rep("02WS", 10000), rep("03S", 10000), rep("03VS", 10000)), 3)
#species.depth <- rep("deep", 120000)
#species.height <- c(rep("01recent", 40000), rep("02medium", 40000), rep("03ancient", 40000))
#treatment <-c(rep("01N_1_E_1", 10000),rep("02S_1_E_1", 10000),rep("03S_1_E_2", 10000),rep("04S_1_E_3", 10000),rep("05N_2_E_1", 10000),rep("06S_2_E_1", 10000),rep("07S_2_E_2", 10000),rep("08S_2_E_3", 10000),rep("09N_3_E_1", 10000),rep("10S_3_E_1", 10000),rep("11S_3_E_2", 10000),rep("12S_3_E_3", 10000))
#FST_AB.df <- data.frame(treatment=treatment, selection.strength =selection.strength, species.depth=species.depth, species.height=species.height, FST_AB.vec=FST_AB.vec)
#
#
#
#ggplot(FST_AB.df, aes(factor(species.height), FST_AB.vec, fill=selection.strength, alpha=selection.strength)) + 
#	stat_boxplot(geom ='errorbar') + geom_boxplot()+theme_bw()+ theme(legend.position="none")
#
#
#
####################
#
#
#FST_BC.vec <- c(N_1_E_1.FST_BC.handle[,1],S_1_E_1.FST_BC.handle[,1],S_1_E_2.FST_BC.handle[,1],S_1_E_3.FST_BC.handle[,1],N_2_E_1.FST_BC.handle[,1],S_2_E_1.FST_BC.handle[,1],S_2_E_2.FST_BC.handle[,1],S_2_E_3.FST_BC.handle[,1],N_3_E_1.FST_BC.handle[,1],S_3_E_1.FST_BC.handle[,1],S_3_E_2.FST_BC.handle[,1],S_3_E_3.FST_BC.handle[,1])
#selection.strength = rep(c(rep("01N", 10000),rep("02WS", 10000), rep("03S", 10000), rep("03VS", 10000)), 3)
#species.depth <- rep("shallow", 120000)
#species.height <- c(rep("01recent", 40000), rep("02medium", 40000), rep("03ancient", 40000))
#treatment <-c(rep("01N_1_E_1", 10000),rep("02S_1_E_1", 10000),rep("03S_1_E_2", 10000),rep("04S_1_E_3", 10000),rep("05N_2_E_1", 10000),rep("06S_2_E_1", 10000),rep("07S_2_E_2", 10000),rep("08S_2_E_3", 10000),rep("09N_3_E_1", 10000),rep("10S_3_E_1", 10000),rep("11S_3_E_2", 10000),rep("12S_3_E_3", 10000))
#FST_BC.df <- data.frame(treatment=treatment, selection.strength =selection.strength, species.depth=species.depth, species.height=species.height, FST_BC.vec=FST_BC.vec)
#
#
#
#ggplot(FST_BC.df, aes(factor(species.height), FST_BC.vec, fill=selection.strength, alpha=selection.strength)) + 
#	stat_boxplot(geom ='errorbar') + geom_boxplot()+theme_bw()+ theme(legend.position="none")
#
################
#
#FST_BC.vec <- c(N_4_E_1.FST_BC.handle[,1],S_4_E_1.FST_BC.handle[,1],S_4_E_2.FST_BC.handle[,1],S_4_E_3.FST_BC.handle[,1],N_5_E_1.FST_BC.handle[,1],S_5_E_1.FST_BC.handle[,1],S_5_E_2.FST_BC.handle[,1],S_5_E_3.FST_BC.handle[,1],N_6_E_1.FST_BC.handle[,1],S_6_E_1.FST_BC.handle[,1],S_6_E_2.FST_BC.handle[,1],S_6_E_3.FST_BC.handle[,1])
#selection.strength = rep(c(rep("01N", 10000),rep("02WS", 10000), rep("03S", 10000), rep("03VS", 10000)), 3)
#species.depth <- rep("moderate", 120000)
#species.height <- c(rep("01recent", 40000), rep("02medium", 40000), rep("03ancient", 40000))
#treatment <-c(rep("01N_1_E_1", 10000),rep("02S_1_E_1", 10000),rep("03S_1_E_2", 10000),rep("04S_1_E_3", 10000),rep("05N_2_E_1", 10000),rep("06S_2_E_1", 10000),rep("07S_2_E_2", 10000),rep("08S_2_E_3", 10000),rep("09N_3_E_1", 10000),rep("10S_3_E_1", 10000),rep("11S_3_E_2", 10000),rep("12S_3_E_3", 10000))
#FST_BC.df <- data.frame(treatment=treatment, selection.strength =selection.strength, species.depth=species.depth, species.height=species.height, FST_BC.vec=FST_BC.vec)
#
#
#
#ggplot(FST_BC.df, aes(factor(species.height), FST_BC.vec, fill=selection.strength, alpha=selection.strength)) + 
#	stat_boxplot(geom ='errorbar') + geom_boxplot()+theme_bw()+ theme(legend.position="none")
#
#
##############
#
#
#FST_BC.vec <- c(N_7_E_1.FST_BC.handle[,1],S_7_E_1.FST_BC.handle[,1],S_7_E_2.FST_BC.handle[,1],S_7_E_3.FST_BC.handle[,1],N_8_E_1.FST_BC.handle[,1],S_8_E_1.FST_BC.handle[,1],S_8_E_2.FST_BC.handle[,1],S_8_E_3.FST_BC.handle[,1],N_9_E_1.FST_BC.handle[,1],S_9_E_1.FST_BC.handle[,1],S_9_E_2.FST_BC.handle[,1],S_9_E_3.FST_BC.handle[,1])
#
#selection.strength = rep(c(rep("01N", 10000),rep("02WS", 10000), rep("03S", 10000), rep("03VS", 10000)), 3)
#species.depth <- rep("deep", 120000)
#species.height <- c(rep("01recent", 40000), rep("02medium", 40000), rep("03ancient", 40000))
#treatment <-c(rep("01N_1_E_1", 10000),rep("02S_1_E_1", 10000),rep("03S_1_E_2", 10000),rep("04S_1_E_3", 10000),rep("05N_2_E_1", 10000),rep("06S_2_E_1", 10000),rep("07S_2_E_2", 10000),rep("08S_2_E_3", 10000),rep("09N_3_E_1", 10000),rep("10S_3_E_1", 10000),rep("11S_3_E_2", 10000),rep("12S_3_E_3", 10000))
#FST_BC.df <- data.frame(treatment=treatment, selection.strength =selection.strength, species.depth=species.depth, species.height=species.height, FST_BC.vec=FST_BC.vec)
#
#
#
#ggplot(FST_BC.df, aes(factor(species.height), FST_BC.vec, fill=selection.strength, alpha=selection.strength)) + 
#	stat_boxplot(geom ='errorbar') + geom_boxplot()+theme_bw()+ theme(legend.position="none")
#
#