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rustAnalyses.R
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rustAnalyses.R
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# Effects of genotype x arrival order interactions on rust severity
# Analyses conducted separately for resistant and susceptible genotypes (likely representing variation in major gene resistance)
library(tidyverse)
library(magrittr)
library(betareg)
library(emmeans)
library(lmtest)
library(ggthemes)
library(patchwork)
library(ggtext)
library(gt)
source("code/Rfunctions.R")
source("code/colors.R")
# load rust data and subset to inoculated plants
rust <- loadRust() %>% filter(Treatment!="Control")
# subset susceptible and resistant genotypes
susceptible <- read.csv("output/tabs/susceptibility.csv", stringsAsFactors = F)
susceptible$Genotype %<>% factor(.,levels=.[order(susceptible$pctLesion)])
rust.s <- rust %>%
filter(Genotype %in% filter(susceptible,Cluster=="susceptible")$Genotype) %>%
mutate(Genotype=factor(Genotype, levels=levels(susceptible$Genotype)),
weights=nleaf*length(nleaf)/sum(nleaf)) #proportionality weight for betagreg model
rust.r <- rust %>%
filter(Genotype %in% filter(susceptible,Cluster=="resistant")$Genotype) %>%
mutate(Genotype=factor(Genotype, levels=levels(susceptible$Genotype)),
weights=nleaf*length(nleaf)/sum(nleaf)) #proportionality weight for betagreg model
#############################
### Betaregression models ###
#############################
### Lesions ###
# Susceptible genotypes
lesion.s <- betareg(pctLesion ~ Genotype*Treatment, weights=weights, data=rust.s)
lesion.s.noInt <- betareg(pctLesion ~ Genotype+Treatment, weights=weights, data=rust.s)
susceptible.interaction <- lrtest(lesion.s, lesion.s.noInt) #test interation
susceptible.treatment <- lrtest(lesion.s.noInt, .~. -Treatment) #test treatment
susceptible.genotype <- lrtest(lesion.s.noInt, .~. -Genotype) #test genotype
# Resistant genotypes - precision parameter modeled as function of genotype to account for heteroskedasticity
lesion.r <- betareg(pctLesion ~ Genotype*Treatment|Genotype, weights=weights, data=rust.r)
lesion.r.noInt <- betareg(pctLesion ~ Genotype+Treatment|Genotype, weights=weights, data=rust.r)
resistant.interaction <- lrtest(lesion.r, lesion.r.noInt) #test interation
resistant.treatment<- lrtest(lesion.r.noInt, .~. -Treatment) #test treatment
resistant.genotype <- lrtest(lesion.r.noInt, .~. -Genotype) #test genotype
results.susceptible <- data.frame(group="Susceptible",
Predictor=c("Genotype","Treatment","Genotype:Treatment"),
'ΔDf'=abs(c(susceptible.genotype$Df[2],
susceptible.treatment$Df[2],
susceptible.interaction$Df[2])),
LR=round(c(susceptible.genotype$Chisq[2],
susceptible.treatment$Chisq[2],
susceptible.interaction$Chisq[2]),1),
P=round(c(susceptible.genotype$`Pr(>Chisq)`[2],
susceptible.treatment$`Pr(>Chisq)`[2],
susceptible.interaction$`Pr(>Chisq)`[2]),3))
results.resistant <- data.frame(group="Resistant",
Predictor=c("Genotype","Treatment","Genotype:Treatment"),
'ΔDf'=abs(c(resistant.genotype$Df[2],
resistant.treatment$Df[2],
resistant.interaction$Df[2])),
LR=round(c(resistant.genotype$Chisq[2],
resistant.treatment$Chisq[2],
resistant.interaction$Chisq[2]),1),
P=round(c(resistant.genotype$`Pr(>Chisq)`[2],
resistant.treatment$`Pr(>Chisq)`[2],
resistant.interaction$`Pr(>Chisq)`[2]),3))
# Summarize results
bind_cols(results.susceptible,results.resistant) %>%
select(-group,-group1, -Predictor1) %>%
gt(rowname_col = "Predictor") %>%
tab_spanner(
label = "Susceptible",
columns = vars(ΔDf, LR, P)
) %>%
tab_spanner(
label = "Resistant",
columns = vars(ΔDf1, LR1, P1)
) %>%
cols_label(ΔDf1='ΔDf',
P=md("*P*-value"),
P1=md("*P*-value"),
LR=md("LRT-χ<sup>2<sup>"),
LR1=md("LRT-χ<sup>2<sup>")) %>%
fmt(
columns = vars(P),
fns = function(x) {
ifelse(x>=0.001,
as.character(x),
"< 0.001")
}
) %>%
cols_align("center") %>%
gtsave("output/figs/betaReg.lesion.png")
### Uridinia ###
# Susceptible genotypes
#uridinia.s <- betareg(pctRust ~ Genotype*Treatment, weights=weights, data=rust.s)
#uridinia.s.noInt <- betareg(pctRust ~ Genotype+Treatment, weights=weights, data=rust.s)
#lrtest(uridinia.s, uridinia.s.noInt) #test interation
#lrtest(uridinia.s.noInt, .~. -Treatment) #test treatment
#lrtest(uridinia.s.noInt, .~. -Genotype) #test genotype
# Resistant genotypes
#uridinia.r <- betareg(pctRust ~ Genotype*Treatment|Genotype, weights=weights, data=rust.r)
#uridinia.r.noInt <- betareg(pctRust ~ Genotype+Treatment|Genotype, weights=weights, data=rust.r)
#lrtest(uridinia.r, uridinia.r.noInt) #test interation
#lrtest(uridinia.r.noInt, .~. -Treatment) #test treatment
#lrtest(uridinia.r.noInt, .~. -Genotype) #test genotype
####################
### Make figures ###
####################
# Susceptible genotypes
(fig.a <- emmeans(lesion.s, ~Treatment|Genotype) %>% data.frame %>%
mutate(Genotype=factor(Genotype,levels=levels(susceptible$Genotype)),
upper.CL=asymp.UCL,
lower.CL=asymp.LCL) %>%
ggplot(aes(x=Treatment,y=emmean,fill=Treatment)) +
geom_hline(data=filter(susceptible,Cluster=="susceptible"),
aes(yintercept=pctLesion),linetype="dotted")+
geom_errorbar(aes(ymin=lower.CL,ymax=upper.CL),width=0)+
geom_point(shape=21,size=2)+
geom_point(data=rust.s,
aes(y=pctLesion,alpha=nleaf),shape=21,size=1,
show.legend = F)+
scale_alpha(range=c(0.4,1))+
labs(y="Rust lesion (%)")+
scale_fill_manual("Initial colonist:",values=pal.treatment)+
scale_y_continuous(labels = function(x) x*100)+
#coord_equal(20)+
ggtitle("Rust susceptible genotypes")+
facet_wrap(~Genotype,nrow=1)+
theme_few()+
theme(strip.background = element_blank(),
axis.text.x = element_blank(),
strip.text = element_text(size=9),
axis.ticks.x = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_markdown(size=9),
legend.text = element_text(size=9,face="italic")))
# Resistant genotypes
(fig.b <- emmeans(lesion.r.noInt, ~Treatment|Genotype) %>% data.frame %>%
mutate(Genotype=factor(Genotype,levels=levels(susceptible$Genotype)),
upper.CL=asymp.UCL,
lower.CL=asymp.LCL) %>%
ggplot(aes(x=Treatment,y=emmean,fill=Treatment)) +
geom_hline(data=filter(susceptible,Cluster=="resistant"),
aes(yintercept=pctLesion),linetype="dotted")+
geom_errorbar(aes(ymin=lower.CL,ymax=upper.CL),width=0)+
geom_point(shape=21,size=2)+
geom_point(data=rust.r,
aes(y=pctLesion,alpha=nleaf),shape=21,size=1,
show.legend = F)+
scale_alpha(range=c(0.4,1))+
labs(y="Rust lesion (%)")+
scale_y_continuous(limits=c(0,0.14),
breaks=c(0,0.1),
labels = function(x) x*100)+
scale_fill_manual("Initial colonist:",values=pal.treatment)+
ggtitle("Rust resistant genotypes")+
facet_wrap(~Genotype,nrow=1)+
theme_few()+
theme(strip.background = element_blank(),
strip.text = element_text(size=9),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_markdown(size=9),
legend.text = element_text(size=9,face="italic")))
# Combine into multipanel figure
fig.a / fig.b +
plot_layout(guides = 'collect',heights = c(4,1.35)) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size=10,face="bold"),
legend.position = 'bottom', legend.title = element_text(size=9),
plot.title = element_text(size=10,hjust=0.5))
ggsave("output/figs/Fig.4.pdf",width=174,height=110,units="mm")