video_code.Rmd

---
title: "SCIP barplot"
output: html_notebook
---


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

```{r}
Tab <- read_tsv("data/rhizo/otu_table.tsv",
                col_types = cols(otu_id = col_character(),
                                 .default = col_number()))
Tab
```



```{r}
dat <- Tab %>%
  pivot_longer(-otu_id, names_to = "sample_id", values_to = "count")
dat
```


```{r}
Tax <- read_tsv("data/rhizo/otu_taxonomy.tsv",
                col_types = cols(.default = "character"))
Tax
```

```{r}
dat <- dat %>%
  left_join(Tax, by = "otu_id")
dat
```

```{r}
Meta <- read_tsv("data/rhizo/sample_metadata.tsv",
                 col_types = cols(.default = col_character()))
Meta
```


```{r}
dat <- dat %>%
  left_join(Meta, by = "sample_id")
dat
```

```{r}
dat %>%
  ggplot(aes(x = sample_id, y = count)) +
  facet_grid(~ fraction + soil, scales = "free_x", space = "free_x") +
  geom_bar(aes(fill = Phylum), stat = "identity", position = "fill", width = 1)
```

```{r}
dat %>%
  ggplot(aes(x = sample_id, y = count)) +
  facet_grid(~ fraction + soil, scales = "free_x", space = "free_x") +
  geom_bar(aes(fill = Phylum), stat = "identity", position = "fill", width = 1) +
  scale_fill_brewer(palette = "Paired")
```


```{r}
phyla_order <- c("Proteobacteria",
		 "Actinobacteria",
		 "Bacteroidetes",
		 "Acidobacteria",
		 "Firmicutes",
		 "Cyanobacteria",
		 "Verrucomicrobia",
		 "Gemmatimonadetes",
		 "Armatimonadetes",
		 "Chloroflexi",
		 "unclassified")
dat <- dat %>%
  mutate(Phylum = factor(Phylum, levels = phyla_order))
```




```{r}
dat %>%
  ggplot(aes(x = sample_id, y = count)) +
  facet_grid(~ fraction + soil, scales = "free_x", space = "free_x") +
  geom_bar(aes(fill = Phylum), stat = "identity", position = "fill", width = 1) +
  scale_fill_brewer(palette = "Paired") +
  scale_y_continuous(name = "Relative abundance",
                     labels = scales::percent) +
  theme(axis.text.x = element_text(angle = 90, size = 6),
        axis.text.y = element_text(color = "black"),
        strip.text = element_text(face = "bold"),
        strip.background = element_blank())
```