sup8.diversity_after_antibiotics.Rmd

---
title: "Violin plots showing the distribution of genus-level diversity metrics for various culture-enriched communities"
output:
  html_document:
    df_print: paged
---

### Nanopore diversity plot

Load generic libraries
```{r}
source('configuration.r')
```

Load plot specific libraries
```{r message=FALSE}
library(vegan)
library(reshape2)
```

Sup. Fig. 6
```{r}
df.mapping <- read.table('../metadata/nanopore.metadata.txt',head=T,sep='\t')
df.nanopore <- read.table('../tables/nanopore.kraken.table.g',head=T,sep='\t',row.names=1)
df.nanopore[df.nanopore < 0.1] <- 0
df.nanopore <- df.nanopore[rowSums(df.nanopore)>0, ]
shan=data.frame(diversity(t(df.nanopore),index="shannon"))
simp=data.frame(diversity(t(df.nanopore),index="simpson"))
shan= mutate(shan,Library=rownames(shan))
simp= mutate(simp,Library=rownames(simp))
colnames(shan)[1]="Shannon"
colnames(simp)[1]="Simpson"
diversity=merge(shan,df.mapping,by.x="Library",by.y="Nanopore_ID")
diversity=merge(diversity,simp,by="Library")
diversity1=select(diversity,Antibiotics,Simpson,Shannon)
diversity1=melt(diversity1,id="Antibiotics")
level_order <- c('BHI', 'AMP', 'CHLOR', 'KAN', 'STREP', 'TET')
diversity1 <- mutate(diversity1, Antibiotics=factor(Antibiotics,level=level_order, ordered = T))

g.a <- ggplot(data = diversity1, aes(x=Antibiotics,y=value,fill=Antibiotics)) +
  geom_violin() +
  theme(axis.text.x = element_text(angle=40, hjust=1, size=18)) +
  scale_fill_manual(values=pal_simpsons(c("springfield"))(16)[-c(2,8)])+
  labs(x='Antibiotics', y='Diversity') + 
  facet_wrap(~variable,nrow=2,scale="free_y")
g.a
```

Save plot
```{r fig.height=10, fig.width=10}
ggsave('../plots/sup8.svg', g.a, width = 10, height = 5)
```


### Session informaton
```{r}
sessionInfo()
```