Fig3B-abundance_stacked_barplot.Rmd

---
title: "Stacked barplot of hgcA abundance"
---

```{r}
library(tidyverse)
setwd("D:/Biology_data/movedtosync/3.Bluehole-Hg/hgcA_abundance")
```

```{r}
# Read in the data
hgcA_abundance <- read_tsv("all-hgcA-abundance.tab")
head(hgcA_abundance)
```

```{r}
# drop the first column
tax_df <- hgcA_abundance %>% select(-hgcA)

# group by the Taxonomy
tax_df <- tax_df %>% group_by(Taxonomy) %>% summarise_all(sum)
tax_df
```
# convert to long format
```{r}
tax_df_long <- tax_df %>% gather(key = "Sample", value = "Abundance", -Taxonomy)
tax_df_long <- tax_df_long %>% separate(Sample, c("Sample_type", "Sample_depth"), sep = "_", convert = TRUE)
tax_df_long
```

# drop the 'm' from the Sample_depth column and convert to numeric
```{r}
tax_df_long$Sample_depth <- as.numeric(gsub("m", "", tax_df_long$Sample_depth))
tax_df_long$Sample_type <- factor(tax_df_long$Sample_type, levels = c("PA", "FL"))
```

# plot the facet stacked barplot
```{r}
ggplot(tax_df_long, aes(x = Sample_type, y = Abundance, fill = Taxonomy)) +
  geom_bar(stat = "identity") +
  facet_wrap(~Sample_depth, ncol = 1, strip.position = "right") +
  theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
  labs( x = "Life style", y = "Relative abundance")+
  scale_fill_manual(values = c(
                                "Bacteroidetes"="#efec5e",
                                "Chloroflexi"="#33a02c",
                                "Deltaproteobacteria"="#ff7f00",
                                "Marinimicrobia"="#1f78b4",
                                "Myxococcota"="#fdbf6f",
                                "Nitrospina"="#a6cee3",
                                "Others"="#cab2d6",
                                "Planctomycetes"="#b2df8a",
                                "Vecturithrix"="#e31a1c",
                                "Verrucomicrobiota"="#6a3d9a")
                    )+
  coord_flip() +
  theme_bw()
```
# save the plot
```{r}
ggsave("hgcA_abundance_stacked_barplot.png", width = 15, height = 10, units = "cm", dpi = 300)
ggsave("hgcA_abundance_stacked_barplot.pdf", width = 15, height = 10, units = "cm")
```