library(readxl) library(tidyverse) library(janitor) # Tony theme theme_tony <- function(base_size = 15, base_family = "Times") {theme( #legend stuff legend.key = element_rect(fill = "white"), legend.background = element_rect(fill = "white"), legend.text = element_text(size = 15, family = "Times", face = "italic"), legend.title = element_text(size = 15, family = "Times"), # plot layout axis.line = element_line(linetype = "solid"), panel.grid.major = element_line(linetype = "blank"), panel.grid.minor = element_line(linetype = "blank"), panel.background = element_rect(fill = "white"), # axis stuff axis.text = element_text(), axis.title = element_text(size = 15, family = "Times"), # axis.text = element_text(size = 13, family = "Times"), # axis.text = element_text(size = 15, colour = "black", family = "Times", vjust = 0), axis.text.x = element_text(size = 15, family = "Times", vjust = 0, color = "black"), axis.text.y = element_text(size = 15, family = "Times", color = "black"), plot.title = element_text(family = "Times", color = "black"), strip.text = element_text(family = "Times", color = "black"), ) } third <- read.csv("Data/long.csv") third$Day <- as.factor(third$Day) summary(third) hist(third$Aro.NE) hist(log(third$Aro.NE)) hist(third$Dmrt1.NE) hist(log(third$Dmrt1.NE)) Aromatase<-aov(log(Aro.NE)~ Day, data=third) summary(Aromatase) par(mfrow=c(2,2)) plot(Aromatase) hist(resid(Aromatase)) TukeyHSD(Aromatase) Dmrt1<-aov(log(Dmrt1.NE)~ Day, data=third) summary(Dmrt1) par(mfrow=c(2,2)) plot(Dmrt1) hist(resid(Dmrt1)) TukeyHSD(Dmrt1) longdf <- third %>% select(-Clutch) %>% gather(item, value, -Day) ggplot(longdf, aes(x = Day , y = value, fill=item))+ geom_boxplot(position = position_dodge(width = .9)) + labs(x = "Days After Last Heat Wave Day", y = "Normalized Expression") + scale_fill_manual(name = "Gene", labels = c("Aromatase", "Dmrt1"), values=c("white", "gray", "white", "gray", "white", "gray", "white", "gray", "white", "gray")) + annotate("text", x = 0.77, y = .001, label= "AB", family = "Times", size = 4) + annotate("text", x = 1.775, y = .00077, label= "A", family = "Times", size = 4) + annotate("text", x = 2.775, y = .001425, label= "AB", family = "Times", size = 4) + annotate("text", x = 3.775, y = .00065, label= "AB", family = "Times", size = 4) + annotate("text", x = 4.775, y = .00127, label= "B", family = "Times", size = 4) + annotate("text", x = 1.22, y = .0005325, label= "ab", family = "Times", size = 4) + annotate("text", x = 2.225, y = .00017, label= "a", family = "Times", size = 4) + annotate("text", x = 3.225, y = .00032, label= "ab", family = "Times", size = 4) + annotate("text", x = 4.225, y = .00033, label= "ab", family = "Times", size = 4) + annotate("text", x = 5.225, y = .0007, label= "b", family = "Times", size = 4) + theme_tony()