##ANOVA Analyzing Mycoplasma and Psychromonas Proportions from Rubyspira Samples
##Created by: Amanda Zellmer & Shana Goffredi
##Date Created: April 15, 2016
##Date Modified: April 15, 2016

#Read in Data
setwd("C:/Users/xxxxx")
Myco <- read.csv("C:/Users/xxxx/MycoplasmaProp.csv", header=T, sep = ",")
Myco.sub <- subset(Myco, Snail == "Ruby" & Type != "Fecal")

##ANOVA Mycoplasma Proportions
aov.out <- aov(Myco$Mycoplasma ~ Myco$Type)
print(aov.out)
summary(aov.out) #prints p-values!

##ANOVA Psychromonas Proportions
aov.out <- aov(Myco$Psychromonas ~ Myco$Type)
print(aov.out)
summary(aov.out) #prints p-values!

##ANOVA Mycoplasma Proportions in Ruby Alone
aov.out <- aov(Myco.sub$Mycoplasma ~ Myco.sub$Type)
print(aov.out)
summary(aov.out) #prints p-values!

##ANOVA Psychromonas Proportions in Ruby Alone
aov.out <- aov(Myco.sub$Psychromonas ~ Myco.sub$Type)
print(aov.out)
summary(aov.out) #prints p-values!

TypeLevels <- c("Digestive Gland", "Stomach", "Intestine", "Fecal", "Other Snails", "Environment")
Myco$Type <- factor(Myco$Type, levels = TypeLevels)

#Plot Mycoplasma proportion Data in a Boxplot and show the data points
ggplot(data=Myco, aes(x=Type, y=Mycoplasma, color=Snail))+
  geom_boxplot(outlier.shape = NA)+
  geom_jitter(position=position_jitter(0.4))+
  theme_classic(base_size = 20)

#Plot Psychromonas proportion Data in a Boxplot and show the data points
ggplot(data=Myco, aes(x=Type, y=Psychromonas, color=Snail))+
  geom_boxplot(outlier.shape = NA)+
  geom_jitter(position=position_jitter(0.4))+
  theme_classic(base_size = 20)