whatbacteria/README.Rmd at main · PennChopMicrobiomeProgram/whatbacteria · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# whatbacteria

<!-- badges: start -->
  [![R-CMD-check](https://github.com/PennChopMicrobiomeProgram/whatbacteria/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/PennChopMicrobiomeProgram/whatbacteria/actions/workflows/R-CMD-check.yaml)
  <!-- badges: end -->

Taxon phenotype and susceptibility databases for the mirix package.

## Installation

You can install the development version of whatbacteria from
[GitHub](https://github.com/) with:

``` r
# install.packages("pak")
pak::pak("PennChopMicrobiomeProgram/whatbacteria")
```

## Usage

```{r}
library(whatbacteria)
```


To access the databases directly:

```{r}
head(taxon_phenotypes)
head(taxon_susceptibility)
```

To get a particular lineage's susceptibilities:

```{r}
what_antibiotic(
   c("Enterococcus faecalis", "Lactobacillus", "Lactobacillus delbrueckii"),
   "vancomycin")
```

To get a particular lineage's phenotypes:

```{r}
what_phenotype(
   c("Bacteroidetes", "Firmicutes", "Firmicutes; Negativicutes"),
   "gram_stain")
```