05-Shiny-basics.Rmd

# Shiny basics  

The purpose of this chapter is to guide you through various processes that you might need to go through to develop a Shiny R application.  

## Integrating Shiny and AWS data storage  

This section aims to demonstrate how to utilise the Amazon Web Service (AWS) API to load data from an AWS bucket into the R environment. It then provides an example of how to use this protocol within a Shiny web application.  

### Install the `aws.s3` package  

```{r eval=FALSE, include=TRUE}

# install package
install.packages('aws.s3')

# load package
library(aws.s3)

```

### Getting your unique AWS access keys - refer to Sonia for help with this step  

  * From https://docs.aws.amazon.com/IAM/latest/UserGuide/id_credentials_access-keys.html:  
    * AWS access keys allow you to sign programmatic requests to the AWS CLI or AWS API.  
    * Access keys consist of two parts: an access key ID (for example, AKIAIOSFODNN7EXAMPLE) and a secret access key (for example, wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY).  
    * Like a user name and password, you must use both the access key ID and secret access key together to authenticate your requests.  
    * Manage your access keys as securely as you do your user name and password (i.e. include the `.Renviron` file in your `.gitignore` file if this is a project you will be storing in a GitHub repository).  

### Setting up your `.Renviron` file  
  * Once you have your access key, secret access key and AWS default region (see step 1), this is the file that will store this information.
  * Assuming that you are in your working directory/ same directory as your Shiny `app.R` file, run the command `touch ./.Renviron` from the command line to generate the `.Renviron` file.   
  * Then open this file, either on the command line, `vi .Renviron`, or interactively on Rstudio.  
  * To edit on the command line, use hit `ESC` followed by `i` to insert text, then to save and close, `ESC` followed by `:wq`.  
  * Add your access key, secret access key and AWS default region, for example:  

```{r Renviron-example, fig.cap = ".Renviron file example", echo = FALSE}
knitr::include_graphics('figures/05-Shiny-basics/fig1_access_key_example.png')
```

  * Save and close the `.Renviron` file.  

### Loading AWS objects  
  * The following command will load your access keys from your `.Renviron` file in an anonymised format, meaning you can put this in the body of your Shiny `app.R` file.  
  
```{r eval=FALSE, include=TRUE}

Sys.setenv("AWS_ACCESS_KEY_ID"=Sys.getenv("AWS_ACCESS_KEY_ID"),
           "AWS_SECRET_ACCESS_KEY"=Sys.getenv("AWS_SECRET_ACCESS_KEY"),
           "AWS_DEFAULT_REGION"=Sys.getenv("AWS_DEFAULT_REGION"))

```

  * Now you can use the AWS API to access remote files using the `aws.s3` package.  
  * The following example uses the `s3read_using` function and calls `read.csv` on the object specified by the `object` argument.  
  * Other reader functions can be used, such as `readr::read_csv` or `fst::read.fst`.  

```{r eval=FALSE, include=TRUE}

# load aws.s3 library
library(aws.s3)

# read in csv from AWS s3 bucket 
obj1 <- aws.s3::s3read_using(read.csv, object = "s3://your-bucket/dataframe.csv")

```

### Shiny/AWS example

Loading data from AWS in a Shiny `app.R` file

  * `app.R` is the core server/UI file you will have if you are building a Shiny app.  
  * This example `app.R` file includes all the necessary code to load data from an AWS bucket  

```{r eval=FALSE, include=TRUE}

## app.R ##

# load libraries
library(shiny)
library(aws.s3)

# load access keys
Sys.setenv("AWS_ACCESS_KEY_ID"=Sys.getenv("AWS_ACCESS_KEY_ID"),
           "AWS_SECRET_ACCESS_KEY"=Sys.getenv("AWS_SECRET_ACCESS_KEY"),
           "AWS_DEFAULT_REGION"=Sys.getenv("AWS_DEFAULT_REGION"))

# load data from AWS bucket, assign to global 
obj1 <<- aws.s3::s3read_using(read.csv, object = "s3://your-bucket/dataframe.csv")

# define server function
server <- function(input, output) {
  # server code
}

# define UI function
ui <- fluidPage(
  # UI code
)

# run shinyApp function 
shinyApp(ui = ui, server = server)

```