# import library for effect size test: (cohens-d)
library("effectsize")

filename = "/data/HyphaeVsYeast/hypeVsYeast_data_overview.csv"

data = read.csv(filename, dec=",")
summary(data)

# filter the data
data24 = data[data$Group=='24h',]
data72 = data[data$Group=='72h',]

dataALL = data[data$Group=='24h' | data$Group=='72h',]

# 24h - Fungus
boxplot(Fungus.fraction~Genotyp, data=data24)
wilcox.test(Fungus.fraction~Genotyp, data=data24, paired=FALSE)
cohens_d(Fungus.fraction~Genotyp, data=data24, paired=FALSE)

# 24h - Yeast <-> Hyphae
boxplot(Yeast.fraction~Genotyp, data=data24)
wilcox.test(Yeast.fraction~Genotyp, data=data24, paired=FALSE)
#wilcox.test(Hyphae.fraction~Genotyp, data=data24, paired=FALSE)
cohens_d(Yeast.fraction~Genotyp, data=data24, paired=FALSE)

# 72h - Fungus
boxplot(Fungus.fraction~Genotyp, data=data72)
wilcox.test(Fungus.fraction~Genotyp, data=data72, paired=FALSE)
cohens_d(Fungus.fraction~Genotyp, data=data72, paired=FALSE)

# 72h - Yeast <-> Hyphae
boxplot(Yeast.fraction~Genotyp, data=data72)
wilcox.test(Yeast.fraction~Genotyp, data=data72, paired=FALSE)
#wilcox.test(Hyphae.fraction~Genotyp, data=data72, paired=FALSE)
cohens_d(Yeast.fraction~Genotyp, data=data72, paired=FALSE)

######## T-tests ########

# T-test für 24h (nur für Normalverteilungen)
t.test(Fungus.fraction~Genotyp, data=data24, paired=FALSE)
t.test(Yeast.Fraction~Genotyp, data=data24, paired=FALSE)
t.test(Hypqe.Fraction~Genotyp, data=data24, paired=FALSE)
  
# T-test für 72h (nur für Normalverteilungen)
t.test(Fungus.fraction~Genotyp, data=data72, paired=FALSE)
t.test(Yeast.Fraction~Genotyp, data=data72, paired=FALSE)
t.test(Hypqe.Fraction~Genotyp, data=data72, paired=FALSE)

######## all data points grouped by Genotyp ########

# Fungus fraction of ALL valid data by Genotyp
boxplot(Fungus.fraction~Genotyp, data=dataALL)
wilcox.test(Fungus.fraction~Genotyp, data=dataALL, paired=FALSE)
cohens_d(Fungus.fraction~Genotyp, data=dataALL, paired=FALSE)

# Fungus fraction of ALL valid data by time
boxplot(Fungus.fraction~Group, data=dataALL)
wilcox.test(Fungus.fraction~Group, data=dataALL, paired=FALSE)
cohens_d(Fungus.fraction~Group, data=dataALL, paired=FALSE)

# scatter plot
plot(dataALL$Fungus.fraction, y=dataALL$Group)