---
title: 'Lecture 4: Basics of plotting in ggplot2'
author: "Dr Nicolaas Puts and Dr Lucas França"
date: "24 October 2022"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}
library(tidyverse)
```
# Load dataset

```{r}
urlfile <- 'https://raw.githubusercontent.com/HeJasonL/BIG-TAC/main/TutorialData.csv' #this loads a csv file called TutorialData and puts it into urlfile

data <- read.csv(urlfile) %>% 
  as_tibble()
```


# Bar plots

```{r}
data %>% 
  
ggplot(aes(x=GABA,
           fill = Group)) +
  geom_histogram(binwidth = 0.5)
```

# Boxplot

```{r}
data %>% 
  
  ggplot(aes(x = Group,
           y = Sensory1,
           fill = Group)) +

  geom_boxplot()
```

# Scatter plots

```{r}
data %>% 
  
  ggplot(aes(x = Age,
           y = Sensory1)) +

  geom_point(aes(colour = Group))
```


# Transparency

```{r}
data %>% 
  
ggplot(aes(x=GABA)) +
  geom_histogram(aes(fill = Group), 
                 binwidth = 0.5, 
                 alpha = 0.6)
```

# Titles, themes, and labels

```{r}
data %>% 
  ggplot(aes(y = Sensory1,
           x = Group)) +
  geom_boxplot(aes(fill = Group)) +
  theme_bw() +
  xlab("Group") +
  ylab("Sensory Scores") +
  ggtitle("Sensory Scores by group") +
  theme(plot.title = element_text(hjust = 0.5))#align title centerd
```

# Stacking plots

```{r}
library(ggforce)
```

```{r}
data %>% 
  
  ggplot(aes(y = Sensory1,
             x = Group)) +
  geom_boxplot(aes(fill = Group), 
               outlier.shape = NA) +
  ggforce::geom_sina() + 
  
  theme_bw() +
  xlab("Group") +
  ylab("Sensory Scores") +
  ggtitle("Sensory Scores by group") +
  theme(plot.title = element_text(hjust = 0.5))
```

Now let's make a publication-ready beautiful plot

# Colours!!

```{r}
library(paletteer)
```

```{r}
data %>% 
  
  ggplot(aes(y = Sensory1,
             x = Group)) +
  geom_boxplot(aes(fill = Group), 
               outlier.shape = NA) +
  ggforce::geom_sina() + 
  
  theme_bw() +
  xlab("Group") +
  ylab("Sensory Scores") +
  ggtitle("Sensory Scores by group") +
  theme(plot.title = element_text(hjust = 0.5)) + 
  scale_fill_paletteer_d("MetBrewer::Juarez")
```

```{r}
data %>% 
  
  ggplot(aes(y = Sensory1,
             x = Group)) +
  geom_boxplot(aes(color = Group, 
                   fill = Group), 
               width = 0.5, 
               alpha = 0.3) + 
  ggforce::geom_sina(aes(fill = Group, 
                         colour = Group), 
                size = 2, 
                pch = 21, 
                alpha = 0.4, 
                maxwidth = .5) + 
  theme_bw() +
  xlab("Group") +
  ylab("Sensory Scores") +
  ggtitle("Sensory Scores by group") +
  theme(plot.title = element_text(hjust = 0.5)) + 
  scale_fill_paletteer_d("MetBrewer::Juarez") + 
  scale_colour_paletteer_d("MetBrewer::Juarez")
```

```{r}
data %>% 
  
  ggplot(aes(y = Sensory1,
             x = Group)) +
  geom_boxplot(aes(color = Group, 
                   fill = Group), 
               width = 0.5, 
               alpha = 0.3, 
               outlier.shape = NA) + 
  ggforce::geom_sina(aes(fill = Group, 
                         colour = Group), 
                size = 3, 
                pch = 21, 
                alpha = 0.4, 
                maxwidth = .5) + 
  theme_bw() +
  xlab("Group") +
  ylab("Sensory Scores") +
  ggtitle("Sensory Scores by group") +
  theme(plot.title = element_text(hjust = 0.5), 
        text = element_text(size = 24)) + 
  scale_fill_paletteer_d("MetBrewer::Juarez") + 
  scale_colour_paletteer_d("MetBrewer::Juarez")
```

# Legends

```{r}
data %>% 
  
  ggplot(aes(y = Sensory1,
             x = Group)) +
  geom_boxplot(aes(color = Group, 
                   fill = Group), 
               width = 0.5, 
               alpha = 0.3, 
               outlier.shape = NA) + 
  ggforce::geom_sina(aes(fill = Group, 
                         colour = Group), 
                size = 3, 
                pch = 21, 
                alpha = 0.4, 
                maxwidth = .5) + 
  theme_bw() +
  xlab("Group") +
  ylab("Sensory Scores") +
  ggtitle("Sensory Scores by group") +
  theme(plot.title = element_text(hjust = 0.5), 
        text = element_text(size = 24), 
        legend.position = "none") + 
  scale_fill_paletteer_d("MetBrewer::Juarez") + 
  scale_colour_paletteer_d("MetBrewer::Juarez")
```

```{r}
data %>% 
  
  ggplot(aes(y = Sensory1,
             x = Group)) +
  geom_boxplot(aes(color = Group, 
                   fill = Group), 
               width = 0.5, 
               alpha = 0.3, 
               outlier.shape = NA) + 
  ggforce::geom_sina(aes(fill = Group, 
                         colour = Group), 
                size = 3, 
                pch = 21, 
                alpha = 0.4, 
                maxwidth = .5) + 
  theme_bw() +
  xlab("Group") +
  ylab("Sensory Scores") +
  ggtitle("Sensory Scores by group") +
  theme(plot.title = element_text(hjust = 0.5), 
        text = element_text(size = 24), 
        legend.position = c(0.9,0.8)) + 
  scale_fill_paletteer_d("MetBrewer::Juarez") + 
  scale_colour_paletteer_d("MetBrewer::Juarez")
```

```{r}
data %>% 
  
  ggplot(aes(y = Sensory1,
             x = Group)) +
  geom_boxplot(aes(color = Group, 
                   fill = Group), 
               width = 0.5, 
               alpha = 0.3, 
               outlier.shape = NA) + 
  ggforce::geom_sina(aes(fill = Group, 
                         colour = Group), 
                size = 3, 
                pch = 21, 
                alpha = 0.4, 
                maxwidth = .5) + 
  theme_bw() +
  xlab("Group") +
  ylab("Sensory Scores") +
  ggtitle("Sensory Scores by group") +
  theme(plot.title = element_text(hjust = 0.5), 
        text = element_text(size = 24), 
        legend.position = c(0.9,0.9), 
        legend.title = element_blank()) + 
  scale_fill_paletteer_d("MetBrewer::Juarez") + 
  scale_colour_paletteer_d("MetBrewer::Juarez")
```

```{r}
data %>% 
  
  ggplot(aes(y = Sensory1,
             x = Group)) +
  geom_boxplot(aes(color = Group, 
                   fill = Group), 
               width = 0.5, 
               alpha = 0.3, 
               outlier.shape = NA) + 
  ggforce::geom_sina(aes(fill = Group, 
                         colour = Group), 
                size = 3, 
                pch = 21, 
                alpha = 0.4, 
                maxwidth = .5) + 
  theme_bw() +
  xlab("Group") +
  ylab("Sensory Scores") +
  ggtitle("Sensory Scores by group") +
  theme(plot.title = element_text(hjust = 0.5), 
        text = element_text(size = 24), 
        legend.position = c(0.9,0.9), 
        legend.title = element_blank(), 
        legend.background = element_blank()) + 
  scale_fill_paletteer_d("MetBrewer::Juarez") + 
  scale_colour_paletteer_d("MetBrewer::Juarez")
```