index.Rmd

---
title: "Virome..."
author: "Author Names"
date: "2019-03-29"
output: html_document
---

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


```{r}
library(tidyverse)
```


## Import

```{r}
phage_counts <- read_csv("data/phage_counts.csv")
```

## Summarise

```{r}
phage_counts <- phage_counts %>% 
    group_by(subject, arm, timepoint, parent_tax_id) %>% 
    count()
```

Number of unique taxa per patient and timepoint.
```{r}
tax_per_subj <- phage_counts %>% 
    group_by(subject, arm, timepoint) %>% 
    summarise(n_tax = n_distinct(parent_tax_id))
```

Average number of taxa per arm and timepoint
```{r}
tax_per_subj %>% 
    group_by(arm, timepoint) %>% 
    summarise(n_tax = mean(n_tax))
```

Plot mean number of taxa per arm and timepoint:
```{r}
pd <- position_dodge(0.1)
tax_per_subj %>% 
    ggplot(aes(x = timepoint, y = n_tax, color = arm)) +
    stat_summary(fun.data = mean_sdl, fun.args = list(mult = 1), position = pd) +
    stat_summary(fun.y = mean, geom = "line", position = pd) +
    labs(x = "Time, months", y = "Number of parent taxa")
```