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# J.Goedhart | @joachimgoedhart | 2017-03-07
# j.goedhart@uva.nl | http://www.molecularcytology.nl/Joachim/
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# Commands that can be executed in R/Rstudio to create graphs
# Requires the library 'ggplot2': http://ggplot2.org
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# Read the data (should be modified to load data from the correct directory)

data_summary <- read.csv("Documents/R-project/Data_summary.csv")
data_tidy <- read.csv("Documents/R-project/Data_tidy.csv")

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# Plot Bargraph with SEM

ggplot(data_summary, aes(x = Condition, y = mean)) + geom_bar(position = position_dodge(), stat="identity", fill="grey90", color="black", size=1, width=0.6) + geom_errorbar(aes(ymin=mean, ymax=mean+sem), width=.4)+ ggtitle("Barplot & SEM") +
ylim(0,2)+theme_light(base_size = 18) + theme(panel.border = element_rect(size = 0.5, linetype = "solid", colour = "black", fill=NA)) + theme(axis.text.y = element_text(size=18))+ ylab("Value [-]") + theme(aspect.ratio=6/3)

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# Plot the mean with SEM

ggplot(data_summary, aes(x = Condition, y = mean)) + geom_errorbar(aes(ymin=mean, ymax=mean), width=.6) + geom_errorbar(aes(ymin=mean-sem, ymax=mean+sem), width=.4)+ ggtitle("Mean & SEM") +
ylim(0,2)+theme_light(base_size = 18) + theme(panel.border = element_rect(size = 0.5, linetype = "solid", colour = "black", fill=NA)) + theme(axis.text.y = element_text(size=18))+ ylab("Value [-]") + theme(aspect.ratio=6/3)

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# Plot the mean with dots

ggplot(data_summary, aes(x = Condition, y = mean)) + geom_errorbar(aes(ymin=mean, ymax=mean), width=.4, size=1) + geom_jitter(data = data_tidy, aes(Condition, ratio), position=position_jitter(0.3), cex=1, color="grey40")+ ggtitle("Mean & data") + 
ylim(0,2)+theme_light(base_size = 18) + theme(panel.border = element_rect(size = 0.5, linetype = "solid", colour = "black", fill=NA)) + theme(axis.text.y = element_text(size=18))+ ylab("Value [-]") + theme(aspect.ratio=6/3)

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# Plot the median with dots

ggplot(data_summary, aes(x = Condition, y = median)) + geom_errorbar(aes(ymin=median, ymax=median), width=.4) + geom_jitter(data = data_tidy, aes(Condition, ratio), position=position_jitter(0.3), cex=1, color="grey40")+ ggtitle("Median & data") +
ylim(0,2)+theme_light(base_size = 18) + theme(panel.border = element_rect(size = 0.5, linetype = "solid", colour = "black", fill=NA)) + theme(axis.text.y = element_text(size=18))+ ylab("Value [-]") + theme(aspect.ratio=6/3)

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# Plot median with dots and 95%CI

ggplot(data_summary, aes(x = Condition, y = median)) + geom_errorbar(aes(ymin=median-CImedian, ymax=median+CImedian), width=.4, size=1) + geom_jitter(data = data_tidy, aes(Condition, ratio), position=position_jitter(0.3), cex=1, color="grey40")+ ggtitle("95% CI (median) & data") +
ylim(0,2)+theme_light(base_size = 18) + theme(panel.border = element_rect(size = 0.5, linetype = "solid", colour = "black", fill=NA)) + theme(axis.text.y = element_text(size=18))+ ylab("Value [-]") + theme(aspect.ratio=6/3)

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# Plot box&dotplot with notches

ggplot(data_tidy, aes(x = Condition, y = ratio)) + geom_boxplot(fill = "grey90", notch = TRUE, outlier.color=NA, width=0.8, size=0.6)+ geom_jitter(data = data_tidy, aes(Condition, ratio), position=position_jitter(0.3), cex=1, color="grey40")+ ggtitle("Boxplot & data") +
ylim(0,2)+theme_light(base_size = 18) + theme(panel.border = element_rect(size = 0.5, linetype = "solid", colour = "black", fill=NA)) + theme(axis.text.y = element_text(size=18))+ ylab("Value [-]") + theme(aspect.ratio=6/3)



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# Alternatives (that were not used for the animated GIF)
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# Plot mean with dots and 95%CI

ggplot(data_summary, aes(x = Condition, y = mean)) + geom_errorbar(aes(ymin=mean-CI, ymax=mean+CI), width=.4, size=1) + geom_jitter(data = data_tidy, aes(Condition, ratio), position=position_jitter(0.3), cex=1, color="grey40") + ggtitle("95% CI (mean) & data")+
ylim(0,2)+theme_light(base_size = 18) + theme(panel.border = element_rect(size = 0.5, linetype = "solid", colour = "black", fill=NA)) + theme(axis.text.y = element_text(size=18))+ ylab("Value [-]") + theme(aspect.ratio=6/3)