# Paired t-test

# setwd("/Users/nato/Marshall_University/Lectures/2022_Spring_BMR_617/BMR617-2022/images/")
library(tidyverse)

uptake <- read_csv("https://denvirlab.marshall.edu/BMR617-2022/data/Na_Uptake.csv")

uptake <- uptake %>% mutate(Experiment = factor(Experiment)) %>% mutate(Treatment = factor(Treatment))

# Set up the plot components
baseplot <- uptake %>% ggplot(aes(x=Treatment, y=Uptake, fill=Treatment)) + 
  facet_grid(~Model) + 
  scale_fill_brewer(palette="Dark2") +
  ylab('3H-GLC Uptake')

boxp <- geom_boxplot(alpha=0.25)
pointPlot <- geom_point(aes(fill=Treatment, group=Experiment), size=3, shape=21)
linePlot <- geom_line(aes(group=Experiment))

png(file='boxplot.only.png', width=8*960, height=8*480, res=8*72)
print(baseplot + boxp) + 
  theme(axis.text=element_text(size=14),axis.title=element_text(size=16,face="bold"),strip.text.x = element_text(
    size = 14),legend.title = element_text(size=16),legend.text = element_text(size=12))
dev.off()

png(file='boxplot.points.png', width=8*960, height=8*480, res=8*72)
print(baseplot + boxp + pointPlot) + 
  theme(axis.text=element_text(size=14),axis.title=element_text(size=16,face="bold"),strip.text.x = element_text(
    size = 14),legend.title = element_text(size=16),legend.text = element_text(size=12))
dev.off()


png(file='boxplot.points.paired.png', width=8*960, height=8*480, res=8*72)
print(baseplot + boxp + pointPlot + linePlot) + 
  theme(axis.text=element_text(size=14),axis.title=element_text(size=16,face="bold"),strip.text.x = element_text(
    size = 14),legend.title = element_text(size=16),legend.text = element_text(size=12))
dev.off()


png(file='paired.nobox.png', width=8*960, height=8*480, res=8*72)
print(baseplot + pointPlot + linePlot) + 
  theme(axis.text=element_text(size=14),axis.title=element_text(size=16,face="bold"),strip.text.x = element_text(
    size = 14),legend.title = element_text(size=16),legend.text = element_text(size=12))
dev.off()

# Paired t-test:
t.test(Uptake ~ Treatment, paired=T, data=uptake)