Code to plot stacked charts for AST and AMR loci

ast_genes.Rmd

---
title: "Plotting stacked AST/AMR data"
output: html_notebook
---

Read in some data. I've used JSON so I can have the data in this text file
```{r message=FALSE, warning=FALSE}
library(jsonlite)
ast_gene_json <- '[
  {
    "id": "sample1",
    "Drug1": "S",
    "Drug2": "R",
    "Drug3": "R",
    "Carbapenamases": "Gene1"
  },
  {
    "id": "sample2",
    "Drug1": "S",
    "Drug2": "R",
    "Drug3": "R",
    "Carbapenamases": "Gene1"
  },
  {
    "id": "sample3",
    "Drug1": "S",
    "Drug2": "R",
    "Drug3": "R",
    "Carbapenamases": "Gene2"
  },
  {
    "id": "sample4",
    "Drug1": "R",
    "Drug2": "R",
    "Drug3": "R",
    "Carbapenamases": "Gene3"
  },
  {
    "id": "sample5",
    "Drug1": "R",
    "Drug2": "R",
    "Drug3": "R",
    "Carbapenamases": "Gene3"
  },
  {
    "id": "sample6",
    "Drug1": "R",
    "Drug2": "R",
    "Drug3": "R",
    "Carbapenamases": "Gene1, Gene2"
  },
  {
    "id": "sample7",
    "Drug1": "R",
    "Drug2": "R",
    "Drug3": "S",
    "Carbapenamases": "Gene4"
  },
  {
    "id": "sample8",
    "Drug1": "R",
    "Drug2": "R",
    "Drug3": "S",
    "Carbapenamases": "Gene5"
  },
  {
    "id": "sample9",
    "Drug1": "R",
    "Drug2": "R",
    "Drug3": "S",
    "Carbapenamases": "Gene6, Gene 7"
  },
  {
    "id": "sample10",
    "Drug1": "R",
    "Drug2": "R",
    "Drug3": "S",
    "Carbapenamases": "Gene5"
  }
]'
ast_genes <- jsonlite::fromJSON(ast_gene_json)
```

Count numbers of occurences
```{r message=FALSE, warning=FALSE}
library(dplyr)
drug_3_counts <- ast_genes %>% count(Drug3,Carbapenamases, name = "count")
```

Plot stacked data.
Use the fct_relevel function from the forcats library so that S comes before R
```{r message=FALSE, warning=FALSE}
library(forcats)
library(ggplot2)
drug_3_counts %>%
  mutate(Drug3 = fct_relevel(Drug3, "S", "R")) %>%
  ggplot(aes(x = Drug3, y = count , fill = Carbapenamases)) +
    geom_bar(stat="identity")
```