alpha_diversity.Rmd

---
title: "Alpha Diversity"
output:
  workflowr::wflow_html:
    toc: true
editor_options:
  chunk_output_type: console
---

This page contains the investigation of alpha diversity investigations.

```{r data, include=FALSE, echo=FALSE}
##Chunk iptions

# load packages
source("code/load_packages.R")

# get data
source("code/get_cleaned_data.R")

theme_set(theme_bw())
#pal = "Set1"
# scale_colour_discrete <-  function(palname=pal, ...){
#   scale_colour_brewer(palette=palname, ...)
# }
# scale_fill_discrete <-  function(palname=pal, ...){
#   scale_fill_brewer(palette=palname, ...)
# }
knitr::opts_chunk$set(out.width = "225%")
```


# Alpha diversity

## By unique participants

```{r}

plot_data <- microbiome_data$meta.dat

ggplot(plot_data, aes(x=SubjectID3, y=Observed, colour=SubjectID3))+
  geom_point(size=2) +
  labs(x="Subject ID")+
  guides(colour= guide_legend(title = "Subject ID"))+
  theme(axis.text.x = element_text(angle=90, vjust=0.5))
  


```


## Boxplots by week of study

### Observed OTUs

```{r}

ggplot(plot_data, aes(x=Week, y=Observed, colour=SubjectID3))+
  geom_boxplot(aes(group=Week))+
  geom_point(size=2, position="jitter")+
  labs(x="Week of Study")+
  guides(colour= guide_legend(title = "Subject ID"))+
  theme(axis.text.x = element_text(angle = 0, hjust=0.33))


```

### Shannon Index

```{r}

ggplot(plot_data, aes(x=Week, y=Shannon, colour=SubjectID3))+
  geom_boxplot(aes(group=Week))+
  geom_point(size=2, position="jitter")+
  labs(x="Week of Study", y="Shannon Index")+
  guides(colour= guide_legend(title = "Subject ID"))+
  theme(axis.text.x = element_text(angle = 0, hjust=0.33))


```

### Simpson

```{r}

ggplot(plot_data, aes(x=Week, y=Simpson, colour=SubjectID3))+
  geom_boxplot(aes(group=Week))+
  geom_point(size=2, position="jitter")+
  labs(x="Week of Study", y="Simpson")+
  guides(colour= guide_legend(title = "Subject ID"))+
  theme(axis.text.x = element_text(angle = 0, hjust=0.33))


```

# Intervention Effect

## Overall Effect

### Observed OTUs

```{r}

ggplot(plot_data, aes(x=Intervention, y=Observed))+
  geom_boxplot(aes(group=Intervention, color=Intervention))+
  geom_point(position="jitter",aes(color=Intervention))+
  labs(x="Intervention Group")+
  theme(axis.text.x = element_text(angle = 0, hjust=0.33))


```

### Shannon Index

```{r}

ggplot(plot_data, aes(x=Intervention, y=Shannon))+
  geom_boxplot(aes(group=Intervention, color=Intervention))+
  geom_point(position="jitter",aes(color=Intervention))+
  labs(x="Intervention Group")+
  theme(axis.text.x = element_text(angle = 0, hjust=0.33))


```

### Simpson

```{r}

ggplot(plot_data, aes(x=Intervention, y=Simpson))+
  geom_boxplot(aes(group=Intervention, color=Intervention))+
  geom_point(position="jitter",aes(color=Intervention))+
  labs(x="Intervention Group")+
  theme(axis.text.x = element_text(angle = 0, hjust=0.33))


```

## Changes Over Time

### Observed OTUs

```{r}

ggplot(plot_data, aes(x=Intervention, y=Observed))+
  geom_boxplot(aes(group=Intervention, color=Intervention))+
  geom_point(position="jitter",aes(color=Intervention))+
  facet_grid(.~Week)+
  labs(x="Intervention Group by Week")+
  guides(colour= guide_legend(title = "Subject ID"))+
  theme(axis.text.x = element_text(angle = 0, hjust=0.33))


```

### Shannon Index

```{r}

ggplot(plot_data, aes(x=Intervention, y=Shannon))+
  geom_boxplot(aes(group=Intervention, color=Intervention))+
  geom_point(position="jitter",aes(color=Intervention))+
  facet_grid(.~Week)+
  labs(x="Intervention Group by Week")+
  guides(colour= guide_legend(title = "Subject ID"))+
  theme(axis.text.x = element_text(angle = 0, hjust=0.33))


```

### Simpson

```{r}

ggplot(plot_data, aes(x=Intervention, y=Simpson))+
  geom_boxplot(aes(group=Intervention, color=Intervention))+
  geom_point(position="jitter",aes(color=Intervention))+
  facet_grid(.~Week)+
  labs(x="Intervention Group by Week")+
  theme(axis.text.x = element_text(angle = 0, hjust=0.33))


```