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2_heritability_values_per_garden.R
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2_heritability_values_per_garden.R
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# heritability and genetic correlation between traits
## notes
# gw - growth
# bb - budbreak
# bs - budset
# B - lmer family blups (means)
# P - plasticity value for the trait
# setwd("Z:/Anoob/MCMCglmm")
# packages
require(MCMCglmm)
require(lmerTest)
require(dplyr)
require(tidyr)
# data
budset_19 <- read.csv("./trait_data/BudSet_2019.csv")
budset_20 <- read.csv("./trait_data/BudSet_2020.csv")
budbreak_20 <- read.csv("./trait_data/BudBreak_2020_cGDD.csv")
heightGrowth_19 <- read.csv("./trait_data/Growth_2019.csv")
heightGrowth_20 <- read.csv("./trait_data/Growth_2020.csv")
########################################################################################################
#-----------------------------------------------Priors-------------------------------------------------#
########################################################################################################
# set priors
Prior <- list(R=list(V=1, n=0.002), # R - prior on residual variance
G=list(G1=list(V=1, n=0.002), # G prior for random variance # G1 = for first randomeffect, here its Family
G2=list(V=1, n=0.002))) # G2 = for second random effect, here its Population
# parameter expansion - trying a fix for budset and budbreak 2020 data
extPrior1 <- list(R=list(V=1, n=1),
G=list(G1=list(V=1,nu=1,alpha.mu=0,alpha.V=100),
G2=list(V=1,nu=1,alpha.mu=0,alpha.V=100)))
########################################################################################################
#--------------------------------MCMCglmm----Heritability----------------------------------------------#
########################################################################################################
############################################ Budset 2019 ###############################################
## Vermont
bs_19_mod_VT <- readRDS("./heritability_mcmcglmm_outputs/bs_19_mod_VT")
# heritability
bs_19_H2_VT = (2*(bs_19_mod_VT$VCV[,"Family"]) + bs_19_mod_VT$VCV[,"Population"])/ (bs_19_mod_VT$VCV[,"Population"] + bs_19_mod_VT$VCV[,"Family"] + bs_19_mod_VT$VCV[,"Bed"] + bs_19_mod_VT$VCV[,"units"])
mean(bs_19_H2_VT)
bs_19_H2_VT <- (2*(bs_19_mod_VT$VCV[,"Family"]) + bs_19_mod_VT$VCV[,"Population"])/rowSums(bs_19_mod_VT[["VCV"]])
mean(bs_19_H2_VT)
posterior.mode(bs_19_H2_VT)
HPDinterval(bs_19_H2_VT)
hist(bs_19_H2_VT)
plot(density(bs_19_H2_VT))
## Maryland
bs_19_mod_MD <- readRDS("./heritability_mcmcglmm_outputs/bs_19_mod_MD")
# heritability
bs_19_H2_MD <- (2*(bs_19_mod_MD$VCV[,"Family"]) + bs_19_mod_MD$VCV[,"Population"])/rowSums(bs_19_mod_MD[["VCV"]])
mean(bs_19_H2_MD)
posterior.mode(bs_19_H2_MD)
HPDinterval(bs_19_H2_MD)
## North Carolina
bs_19_mod_NC <- readRDS("./heritability_mcmcglmm_outputs/bs_19_mod_NC")
# heritability
bs_19_H2_NC <- (2*(bs_19_mod_NC$VCV[,"Family"]) + bs_19_mod_NC$VCV[,"Population"])/rowSums(bs_19_mod_NC[["VCV"]])
mean(bs_19_H2_NC)
posterior.mode(bs_19_H2_NC)
HPDinterval(bs_19_H2_NC)
############################################ Budset 2020 ###############################################
############################################ normal prior ##############################################
## Vermont
bs_20_mod_VT <- readRDS("./heritability_mcmcglmm_outputs/bs_20_mod_VT")
# diagnostics
plot(bs_20_mod_VT)
effectiveSize(bs_20_mod_VT$VCV)
heidel.diag(bs_20_mod_VT$VCV)
# heritability
bs_20_H2_VT <- (2*(bs_20_mod_VT$VCV[,"Family"]) + bs_20_mod_VT$VCV[,"Population"])/rowSums(bs_20_mod_VT[["VCV"]])
mean(bs_20_H2_VT)
posterior.mode(bs_20_H2_VT)
HPDinterval(bs_20_H2_VT)
plot(bs_20_H2_VT)
## Maryland
bs_20_mod_MD <- readRDS("./heritability_mcmcglmm_outputs/bs_20_mod_MD")
# diagnostics
plot(bs_20_mod_MD)
effectiveSize(bs_20_mod_MD$VCV)
heidel.diag(bs_20_mod_MD$VCV) # failed
# heritability
bs_20_H2_MD <- (2*(bs_20_mod_MD$VCV[,"Family"]) + bs_20_mod_MD$VCV[,"Population"])/rowSums(bs_20_mod_MD[["VCV"]])
mean(bs_20_H2_MD)
posterior.mode(bs_20_H2_MD)
HPDinterval(bs_20_H2_MD)
plot(bs_20_H2_MD)
## North Carolina
bs_20_mod_NC <-readRDS("./heritability_mcmcglmm_outputs/bs_20_mod_NC")
# diagnostics
plot(bs_20_mod_NC)
effectiveSize(bs_20_mod_NC$VCV)
heidel.diag(bs_20_mod_NC$VCV) # failed
# heritability
bs_20_H2_NC <- (2*(bs_20_mod_NC$VCV[,"Family"]) + bs_20_mod_NC$VCV[,"Population"])/rowSums(bs_20_mod_NC[["VCV"]])
mean(bs_20_H2_NC)
posterior.mode(bs_20_H2_NC)
HPDinterval(bs_20_H2_NC)
plot(bs_20_H2_NC)
############################################ extended prior ############################################
## Vermont
bs_20_mod_VT_ext <- readRDS("./heritability_mcmcglmm_outputs/bs_20_mod_VT_ext")
# diagnostics
plot(bs_20_mod_VT_ext)
effectiveSize(bs_20_mod_VT_ext$VCV)
heidel.diag(bs_20_mod_VT_ext$VCV)
# heritability
bs_20_H2_VT_ext <- (2*(bs_20_mod_VT_ext$VCV[,"Family"]) + bs_20_mod_VT_ext$VCV[,"Population"])/rowSums(bs_20_mod_VT_ext[["VCV"]])
mean(bs_20_H2_VT_ext)
posterior.mode(bs_20_H2_VT_ext) #0.04652454
HPDinterval(bs_20_H2_VT_ext) # 0.01004681 0.09119632
plot(bs_20_H2_VT_ext)
hist(bs_20_H2_VT_ext)
## Maryland
bs_20_mod_MD_ext <- readRDS("./heritability_mcmcglmm_outputs/bs_20_mod_MD_ext")
# diagnostics
plot(bs_20_mod_MD_ext)
effectiveSize(bs_20_mod_MD_ext$VCV)
heidel.diag(bs_20_mod_MD_ext$VCV) # passed
# heritability
bs_20_H2_MD_ext <- (2*(bs_20_mod_MD_ext$VCV[,"Family"]) + bs_20_mod_MD_ext$VCV[,"Population"])/rowSums(bs_20_mod_MD_ext[["VCV"]])
mean(bs_20_H2_MD_ext)
posterior.mode(bs_20_H2_MD_ext) #0.1143763
HPDinterval(bs_20_H2_MD_ext) # 0.06623493 0.1676811
plot(bs_20_H2_MD_ext)
hist(bs_20_H2_MD_ext)
## North Carolina
bs_20_mod_NC_ext <- readRDS("./heritability_mcmcglmm_outputs/bs_20_mod_NC_ext")
# diagnostics
plot(bs_20_mod_NC_ext)
effectiveSize(bs_20_mod_NC_ext$VCV)
heidel.diag(bs_20_mod_NC_ext$VCV) # passed
# heritability
bs_20_H2_NC_ext <- (2*(bs_20_mod_NC_ext$VCV[,"Family"]) + bs_20_mod_NC_ext$VCV[,"Population"])/rowSums(bs_20_mod_NC_ext[["VCV"]])
mean(bs_20_H2_NC_ext)
posterior.mode(bs_20_H2_NC_ext) #0.1222343
HPDinterval(bs_20_H2_NC_ext) # 0.06608991 0.1768585
plot(bs_20_H2_NC_ext)
hist(bs_20_H2_NC_ext)
########################################### Budbreak 2020 ##############################################
## Vermont
bb_20_mod_VT <- readRDS("./heritability_mcmcglmm_outputs/bb_20_mod_VT")
# heritability
bb_20_H2_VT <- (2*(bb_20_mod_VT$VCV[,"Family"]) + bb_20_mod_VT$VCV[,"Population"])/rowSums(bb_20_mod_VT[["VCV"]])
mean(bb_20_H2_VT)
posterior.mode(bb_20_H2_VT)
HPDinterval(bb_20_H2_VT)
## Maryland
bb_20_mod_MD <- readRDS("./heritability_mcmcglmm_outputs/bb_20_mod_MD")
# heritability
bb_20_H2_MD <- (2*(bb_20_mod_MD$VCV[,"Family"]) + bb_20_mod_MD$VCV[,"Population"])/rowSums(bb_20_mod_MD[["VCV"]])
mean(bb_20_H2_MD)
posterior.mode(bb_20_H2_MD)
HPDinterval(bb_20_H2_MD)
## North Carolina
bb_20_mod_NC <- readRDS("./heritability_mcmcglmm_outputs/bb_20_mod_NC")
# heritability
bb_20_H2_NC <- (2*(bb_20_mod_NC$VCV[,"Family"]) + bb_20_mod_NC$VCV[,"Population"])/rowSums(bb_20_mod_NC[["VCV"]])
mean(bb_20_H2_NC)
posterior.mode(bb_20_H2_NC)
HPDinterval(bb_20_H2_NC)
############################################ Growth 2019 ###############################################
## Vermont
gw_19_mod_VT <- readRDS("./heritability_mcmcglmm_outputs/gw_19_mod_VT")
# heritability
gw_19_H2_VT <- (2*(gw_19_mod_VT$VCV[,"Family"]) + gw_19_mod_VT$VCV[,"Population"])/rowSums(gw_19_mod_VT[["VCV"]])
mean(gw_19_H2_VT)
posterior.mode(gw_19_H2_VT)
HPDinterval(gw_19_H2_VT)
## Maryland
gw_19_mod_MD <- readRDS("./heritability_mcmcglmm_outputs/gw_19_mod_MD")
# heritability
gw_19_H2_MD <- (2*(gw_19_mod_MD$VCV[,"Family"]) + gw_19_mod_MD$VCV[,"Population"])/rowSums(gw_19_mod_MD[["VCV"]])
mean(gw_19_H2_MD)
posterior.mode(gw_19_H2_MD)
HPDinterval(gw_19_H2_MD)
## North Carolina
gw_19_mod_NC <- readRDS("./heritability_mcmcglmm_outputs/gw_19_mod_NC")
# heritability
gw_19_H2_NC <- (2*(gw_19_mod_NC$VCV[,"Family"]) + gw_19_mod_NC$VCV[,"Population"])/rowSums(gw_19_mod_NC[["VCV"]])
mean(gw_19_H2_NC)
posterior.mode(gw_19_H2_NC)
HPDinterval(gw_19_H2_NC)
############################################ Growth 2020 ###############################################
## Vermont
gw_20_mod_VT <- readRDS("./heritability_mcmcglmm_outputs/gw_20_mod_VT")
# heritability
gw_20_H2_VT <- (2*(gw_20_mod_VT$VCV[,"Family"]) + gw_20_mod_VT$VCV[,"Population"])/rowSums(gw_20_mod_VT[["VCV"]])
mean(gw_20_H2_VT)
posterior.mode(gw_20_H2_VT)
HPDinterval(gw_20_H2_VT)
## Maryland
gw_20_mod_MD <- readRDS("./heritability_mcmcglmm_outputs/gw_20_mod_MD")
# heritability
gw_20_H2_MD <- (2*(gw_20_mod_MD$VCV[,"Family"]) + gw_20_mod_MD$VCV[,"Population"])/rowSums(gw_20_mod_MD[["VCV"]])
mean(gw_20_H2_MD)
posterior.mode(gw_20_H2_MD)
HPDinterval(gw_20_H2_MD)
## North Carolina
gw_20_mod_NC <- readRDS("./heritability_mcmcglmm_outputs/gw_20_mod_NC")
# heritability
gw_20_H2_NC <- (2*(gw_20_mod_NC$VCV[,"Family"]) + gw_20_mod_NC$VCV[,"Population"])/rowSums(gw_20_mod_NC[["VCV"]])
mean(gw_20_H2_NC)
posterior.mode(gw_20_H2_NC)
HPDinterval(gw_20_H2_NC)
########################################################################################################
#--------------------------------lmer--models----Heritability------------------------------------------#
########################################################################################################
############################################ budset 2019 ###############################################
## Vermont
bs_19_VT <- budset_19[budset_19$Garden=="Vermont",]
# lmer model
bs_19_lmer_VT <- lmer(BudSet ~ (1|Family) + (1|Population) + (1|Bed), data=bs_19_VT)
# heritability
as.data.frame(VarCorr(bs_19_lmer_VT))
bs_19_lmer_H2_VT <- as.data.frame(VarCorr(bs_19_lmer_VT))
# or
bs_19_lmer_H2_VT <- as.data.frame(print(bs_19_lmer_H2_VT,comp=c("Variance","Std.Dev")))
bs_19_lmer_H2_VT <- (2*(bs_19_lmer_H2_VT[bs_19_lmer_H2_VT$grp=="Family","vcov"]))/sum(bs_19_lmer_H2_VT$vcov)
bs_19_lmer_H2_VT
## Maryland
bs_19_MD <- budset_19[budset_19$Garden=="Maryland",]
# lmer model
bs_19_lmer_MD <- lmer(BudSet ~ (1|Family) + (1|Population) + (1|Bed), data=bs_19_MD)
# heritability
as.data.frame(VarCorr(bs_19_lmer_MD))
bs_19_lmer_H2_MD <- as.data.frame(VarCorr(bs_19_lmer_MD))
bs_19_lmer_H2_MD <- (2*(bs_19_lmer_H2_MD[bs_19_lmer_H2_MD$grp=="Family","vcov"]))/sum(bs_19_lmer_H2_MD$vcov)
bs_19_lmer_H2_MD
## North Carolina
bs_19_NC <- budset_19[budset_19$Garden=="North_Carolina",]
# lmer model
bs_19_lmer_NC <- lmer(BudSet ~ (1|Family) + (1|Population) + (1|Bed), data=bs_19_NC)
# heritability
as.data.frame(VarCorr(bs_19_lmer_NC))
bs_19_lmer_H2_NC <- as.data.frame(VarCorr(bs_19_lmer_NC))
bs_19_lmer_H2_NC <- (2*(bs_19_lmer_H2_NC[bs_19_lmer_H2_NC$grp=="Family","vcov"]))/sum(bs_19_lmer_H2_NC$vcov)
bs_19_lmer_H2_NC
############################################ budset 2020 ###############################################
## Vermont
bs_20_VT <- budset_20[budset_20$Garden=="Vermont",]
# lmer model
bs_20_lmer_VT <- lmer(BudSet ~ (1|Family) + (1|Population) + (1|Bed), data=bs_20_VT)
# heritability
as.data.frame(VarCorr(bs_20_lmer_VT))
bs_20_lmer_H2_VT <- as.data.frame(VarCorr(bs_20_lmer_VT))
# or
bs_20_lmer_H2_VT <- as.data.frame(print(bs_20_lmer_H2_VT,comp=c("Variance","Std.Dev")))
bs_20_lmer_H2_VT <- (2*(bs_20_lmer_H2_VT[bs_20_lmer_H2_VT$grp=="Family","vcov"]))/sum(bs_20_lmer_H2_VT$vcov)
bs_20_lmer_H2_VT
## Maryland
bs_20_MD <- budset_20[budset_20$Garden=="Maryland",]
# lmer model
bs_20_lmer_MD <- lmer(BudSet ~ (1|Family) + (1|Population) + (1|Bed), data=bs_20_MD)
# heritability
as.data.frame(VarCorr(bs_20_lmer_MD))
bs_20_lmer_H2_MD <- as.data.frame(VarCorr(bs_20_lmer_MD))
bs_20_lmer_H2_MD <- (2*(bs_20_lmer_H2_MD[bs_20_lmer_H2_MD$grp=="Family","vcov"]))/sum(bs_20_lmer_H2_MD$vcov)
bs_20_lmer_H2_MD
## North Carolina
bs_20_NC <- budset_20[budset_20$Garden=="North_Carolina",]
# lmer model
bs_20_lmer_NC <- lmer(BudSet ~ (1|Family) + (1|Population) + (1|Bed), data=bs_20_NC)
# heritability
as.data.frame(VarCorr(bs_20_lmer_NC))
bs_20_lmer_H2_NC <- as.data.frame(VarCorr(bs_20_lmer_NC))
bs_20_lmer_H2_NC <- (2*(bs_20_lmer_H2_NC[bs_20_lmer_H2_NC$grp=="Family","vcov"]))/sum(bs_20_lmer_H2_NC$vcov)
bs_20_lmer_H2_NC
############################################ budbreak 2020 ###############################################
## Vermont
bb_20_VT <- budbreak_20[budbreak_20$Garden=="Vermont",]
# lmer model
bb_20_lmer_VT <- lmer(cGDD ~ (1|Family) + (1|Population) + (1|Bed), data=bb_20_VT)
# heritability
as.data.frame(VarCorr(bb_20_lmer_VT))
bb_20_lmer_H2_VT <- as.data.frame(VarCorr(bb_20_lmer_VT))
# or
bb_20_lmer_H2_VT <- as.data.frame(print(bb_20_lmer_H2_VT,comp=c("Variance","Std.Dev")))
bb_20_lmer_H2_VT <- (2*(bb_20_lmer_H2_VT[bb_20_lmer_H2_VT$grp=="Family","vcov"]))/sum(bb_20_lmer_H2_VT$vcov)
bb_20_lmer_H2_VT
## Maryland
bb_20_MD <- budbreak_20[budbreak_20$Garden=="Maryland",]
# lmer model
bb_20_lmer_MD <- lmer(cGDD ~ (1|Family) + (1|Population) + (1|Bed), data=bb_20_MD)
# heritability
as.data.frame(VarCorr(bb_20_lmer_MD))
bb_20_lmer_H2_MD <- as.data.frame(VarCorr(bb_20_lmer_MD))
bb_20_lmer_H2_MD <- (2*(bb_20_lmer_H2_MD[bb_20_lmer_H2_MD$grp=="Family","vcov"]))/sum(bb_20_lmer_H2_MD$vcov)
bb_20_lmer_H2_MD
## North Carolina
bb_20_NC <- budbreak_20[budbreak_20$Garden=="North_Carolina",]
# lmer model
bb_20_lmer_NC <- lmer(cGDD ~ (1|Family) + (1|Population) + (1|Bed), data=bb_20_NC)
# heritability
as.data.frame(VarCorr(bb_20_lmer_NC))
bb_20_lmer_H2_NC <- as.data.frame(VarCorr(bb_20_lmer_NC))
bb_20_lmer_H2_NC <- (2*(bb_20_lmer_H2_NC[bb_20_lmer_H2_NC$grp=="Family","vcov"]))/sum(bb_20_lmer_H2_NC$vcov)
bb_20_lmer_H2_NC
############################################ Growth 2019 ###############################################
## Vermont
gw_19_VT <- heightGrowth_19[heightGrowth_19$Garden=="Vermont",]
# lmer model
gw_19_lmer_VT <- lmer(Growth ~ (1|Family) + (1|Population) + (1|Bed), data=gw_19_VT)
# heritability
as.data.frame(VarCorr(gw_19_lmer_VT))
gw_19_lmer_H2_VT <- as.data.frame(VarCorr(gw_19_lmer_VT))
# or
gw_19_lmer_H2_VT <- as.data.frame(print(gw_19_lmer_H2_VT,comp=c("Variance","Std.Dev")))
gw_19_lmer_H2_VT <- (2*(gw_19_lmer_H2_VT[gw_19_lmer_H2_VT$grp=="Family","vcov"]))/sum(gw_19_lmer_H2_VT$vcov)
gw_19_lmer_H2_VT
## Maryland
gw_19_MD <- heightGrowth_19[heightGrowth_19$Garden=="Maryland",]
# lmer model
gw_19_lmer_MD <- lmer(Growth ~ (1|Family) + (1|Population) + (1|Bed), data=gw_19_MD)
# heritability
as.data.frame(VarCorr(gw_19_lmer_MD))
gw_19_lmer_H2_MD <- as.data.frame(VarCorr(gw_19_lmer_MD))
gw_19_lmer_H2_MD <- (2*(gw_19_lmer_H2_MD[gw_19_lmer_H2_MD$grp=="Family","vcov"]))/sum(gw_19_lmer_H2_MD$vcov)
gw_19_lmer_H2_MD
## North Carolina
gw_19_NC <- heightGrowth_19[heightGrowth_19$Garden=="North_Carolina",]
# lmer model
gw_19_lmer_NC <- lmer(Growth ~ (1|Family) + (1|Population) + (1|Bed), data=gw_19_NC)
# heritability
as.data.frame(VarCorr(gw_19_lmer_NC))
gw_19_lmer_H2_NC <- as.data.frame(VarCorr(gw_19_lmer_NC))
gw_19_lmer_H2_NC <- (2*(gw_19_lmer_H2_NC[gw_19_lmer_H2_NC$grp=="Family","vcov"]))/sum(gw_19_lmer_H2_NC$vcov)
gw_19_lmer_H2_NC
############################################ Growth 2020 ###############################################
## Vermont
gw_20_VT <- heightGrowth_20[heightGrowth_20$Garden=="Vermont",]
# lmer model
gw_20_lmer_VT <- lmer(Growth ~ (1|Family) + (1|Population) + (1|Bed), data=gw_20_VT)
# heritability
as.data.frame(VarCorr(gw_20_lmer_VT))
gw_20_lmer_H2_VT <- as.data.frame(VarCorr(gw_20_lmer_VT))
# or
gw_20_lmer_H2_VT <- as.data.frame(print(gw_20_lmer_H2_VT,comp=c("Variance","Std.Dev")))
gw_20_lmer_H2_VT <- (2*(gw_20_lmer_H2_VT[gw_20_lmer_H2_VT$grp=="Family","vcov"]))/sum(gw_20_lmer_H2_VT$vcov)
gw_20_lmer_H2_VT
## Maryland
gw_20_MD <- heightGrowth_20[heightGrowth_20$Garden=="Maryland",]
# lmer model
gw_20_lmer_MD <- lmer(Growth ~ (1|Family) + (1|Population) + (1|Bed), data=gw_20_MD)
# heritability
as.data.frame(VarCorr(gw_20_lmer_MD))
gw_20_lmer_H2_MD <- as.data.frame(VarCorr(gw_20_lmer_MD))
gw_20_lmer_H2_MD <- (2*(gw_20_lmer_H2_MD[gw_20_lmer_H2_MD$grp=="Family","vcov"]))/sum(gw_20_lmer_H2_MD$vcov)
gw_20_lmer_H2_MD
## North Carolina
gw_20_NC <- heightGrowth_20[heightGrowth_20$Garden=="North_Carolina",]
# lmer model
gw_20_lmer_NC <- lmer(Growth ~ (1|Family) + (1|Population) + (1|Bed), data=gw_20_NC)
# heritability
as.data.frame(VarCorr(gw_20_lmer_NC))
gw_20_lmer_H2_NC <- as.data.frame(VarCorr(gw_20_lmer_NC))
gw_20_lmer_H2_NC <- (2*(gw_20_lmer_H2_NC[gw_20_lmer_H2_NC$grp=="Family","vcov"]))/sum(gw_20_lmer_H2_NC$vcov)
gw_20_lmer_H2_NC
###########################################################################################################
################################## Heritability and correlation plots #####################################
###########################################################################################################
corrplot <- data.frame("Trait" = c("Budset_2019", "Budset_2020", "Budbreak_2020", "Growth_2019", "Growth_2020"),
"Budset_2019" = c(1, 0.22, 0.255, 0.594, NA),
"Budset_2020" = c(0.322, 1, 0.002, NA, 0.493),
"Budbreak_2020" = c(0.884, 0.085, 1, 0.339, 0.0466),
"Growth_2019" = c(0.67, NA, 0.567, 1, 0.433),
"Growth_2020" = c(NA, 0.852, -0.189, 0.676, 1))
require(corrplot)
corrplot(corrplot, method="circle")
require(GGally)
ggcorr(corrplot, method = c("everything", "pearson"))
ggpairs(corrplot)
# budset 2019
Budset_2019_VT <- NULL
Budset_2019_VT$Value <- c(bs_19_H2_VT)
Budset_2019_VT$Garden <- "Vermont"
Budset_2019_VT$Trait <- "Budset_2019"
Budset_2019_VT <- as.data.frame(Budset_2019_VT)
Budset_2019_MD <- NULL
Budset_2019_MD$Value <- c(bs_19_H2_MD)
Budset_2019_MD$Garden <- "Maryland"
Budset_2019_MD$Trait <- "Budset_2019"
Budset_2019_MD <- as.data.frame(Budset_2019_MD)
Budset_2019_NC <- NULL
Budset_2019_NC$Value <- c(bs_19_H2_NC)
Budset_2019_NC$Garden <- "North_Carolina"
Budset_2019_NC$Trait <- "Budset_2019"
Budset_2019_NC <- as.data.frame(Budset_2019_NC)
# budset 2020
Budset_2020_VT <- NULL
Budset_2020_VT$Value <- c(bs_20_H2_VT_ext)
Budset_2020_VT$Garden <- "Vermont"
Budset_2020_VT$Trait <- "Budset_2020"
Budset_2020_VT <- as.data.frame(Budset_2020_VT)
Budset_2020_MD <- NULL
Budset_2020_MD$Value <- c(bs_20_H2_MD_ext)
Budset_2020_MD$Garden <- "Maryland"
Budset_2020_MD$Trait <- "Budset_2020"
Budset_2020_MD <- as.data.frame(Budset_2020_MD)
Budset_2020_NC <- NULL
Budset_2020_NC$Value <- c(bs_20_H2_NC_ext)
Budset_2020_NC$Garden <- "North_Carolina"
Budset_2020_NC$Trait <- "Budset_2020"
Budset_2020_NC <- as.data.frame(Budset_2020_NC)
# budbreak 2020
Budbreak_2020_VT <- NULL
Budbreak_2020_VT$Value <- c(bb_20_H2_VT) # edit
Budbreak_2020_VT$Garden <- "Vermont"
Budbreak_2020_VT$Trait <- "Budbreak_2020"
Budbreak_2020_VT <- as.data.frame(Budbreak_2020_VT)
Budbreak_2020_MD <- NULL
Budbreak_2020_MD$Value <- c(bb_20_H2_MD)
Budbreak_2020_MD$Garden <- "Maryland"
Budbreak_2020_MD$Trait <- "Budbreak_2020"
Budbreak_2020_MD <- as.data.frame(Budbreak_2020_MD)
Budbreak_2020_NC <- NULL
Budbreak_2020_NC$Value <- c(bb_20_H2_NC)
Budbreak_2020_NC$Garden <- "North_Carolina"
Budbreak_2020_NC$Trait <- "Budbreak_2020"
Budbreak_2020_NC <- as.data.frame(Budbreak_2020_NC)
# growth 2019
Growth_2019_VT <- NULL
Growth_2019_VT$Value <- c(gw_19_H2_VT)
Growth_2019_VT$Garden <- "Vermont"
Growth_2019_VT$Trait <- "Growth_2019"
Growth_2019_VT <- as.data.frame(Growth_2019_VT)
Growth_2019_MD <- NULL
Growth_2019_MD$Value <- c(gw_19_H2_MD)
Growth_2019_MD$Garden <- "Maryland"
Growth_2019_MD$Trait <- "Growth_2019"
Growth_2019_MD <- as.data.frame(Growth_2019_MD)
Growth_2019_NC <- NULL
Growth_2019_NC$Value <- c(gw_19_H2_NC)
Growth_2019_NC$Garden <- "North_Carolina"
Growth_2019_NC$Trait <- "Growth_2019"
Growth_2019_NC <- as.data.frame(Growth_2019_NC)
# growth 2020
Growth_2020_VT <- NULL
Growth_2020_VT$Value <- c(gw_20_H2_VT)
Growth_2020_VT$Garden <- "Vermont"
Growth_2020_VT$Trait <- "Growth_2020"
Growth_2020_VT <- as.data.frame(Growth_2020_VT)
Growth_2020_MD <- NULL
Growth_2020_MD$Value <- c(gw_20_H2_MD)
Growth_2020_MD$Garden <- "Maryland"
Growth_2020_MD$Trait <- "Growth_2020"
Growth_2020_MD <- as.data.frame(Growth_2020_MD)
Growth_2020_NC <- NULL
Growth_2020_NC$Value <- c(gw_20_H2_NC)
Growth_2020_NC$Garden <- "North_Carolina"
Growth_2020_NC$Trait <- "Growth_2020"
Growth_2020_NC <- as.data.frame(Growth_2020_NC)
heritabilty <- rbind(Budset_2019_VT,Budset_2019_MD,Budset_2019_NC,
Budset_2020_VT,Budset_2020_MD,Budset_2020_NC,
Budbreak_2020_VT,Budbreak_2020_MD,Budbreak_2020_NC,
Growth_2019_VT,Growth_2019_MD,Growth_2019_NC,
Growth_2020_VT,Growth_2020_MD,Growth_2020_NC)
# write.csv(heritabilty, "./heritability.csv")
heritabilty <- read.csv("./heritability.csv", header=T, stringsAsFactors = T)
require(viridis)
require(tidyverse)
heritabilty$Garden <- as.factor(heritabilty$Garden)
heritabilty$Trait <- as.factor(heritabilty$Trait)
heritabilty$Garden <- factor(heritabilty$Garden,levels = c("Vermont", "Maryland", "North_Carolina"))
heritabilty$Trait <- factor(heritabilty$Trait,levels = c("Budset_2019", "Budset_2020", "Budbreak_2020",
"Growth_2019", "Growth_2020"))
# dodge <- position_dodge(width = 0.4)
ggplot(data=heritabilty,
aes(x=Trait, y=Value, fill=Garden)) +
geom_boxplot(width=0.75, color="grey", alpha=0.8) +
scale_fill_viridis(discrete = TRUE) +
theme(
legend.position="none",
plot.title = element_text(size=11)
) +
theme_bw()
ggplot(data=heritabilty,
aes(x=Trait, y=Value, fill=Garden)) +
scale_fill_viridis_d(option = "D")+
geom_violin(alpha=0.15, position = position_dodge(width = .75),size=0.1,color="black") +
geom_boxplot(notch = TRUE, outlier.size = -1, color="black",lwd=0.2, alpha = 0.7) +
theme_bw() +
labs(x = "Trait", y = "Heritability") +
theme(axis.text=element_text(size=14),
axis.title=element_text(size=14,face="bold"),
legend.title = element_text(color = "black", size = 14),
legend.text = element_text(color = "black", size = 13))