---
title: "Shiny Web Apps"
author: "Thomas Girke"
date: last-modified
sidebar: tutorials
bibliography: bibtex.bib
---

<p align="right">
  <a href="https://raw.githubusercontent.com/tgirke/GEN242/refs/heads/main/tutorials/shinyapps/shinyapps_index.qmd">
    <img src="https://img.shields.io/badge/Download-.qmd-blue?style=for-the-badge&logoColor=white" alt="Download qmd">
  </a>
</p>

```{r setup}
#| echo: false
#| message: false
#| warning: false
suppressPackageStartupMessages({
    library(ggplot2)
})

```


## What is Shiny?

[Shiny](https://shiny.posit.co/r/gallery/) is an R-based environment for building interactive web applications for
data analysis and exploration [@noauthor_undated-mi; @shiny1]. Since most JavaScript code is autogenerated by
the environment, basic R knowledge is sufficient for developing Shiny apps. 
They can be deployed on local computers or web servers including custom and cloud-based servers (e.g.
AWS, GCP, [shinyapps.io](http://www.shinyapps.io/) service). Since 2023, Shiny is also available for
Python — see [Shiny for Python](https://shiny.posit.co/py/) — though this tutorial focuses on the R version.
The basic structure of a Shiny app is an `app.R` script containing the following components:


**Step 1.** User interface
```{r fluidpage}
#| eval: false
ui <- fluidPage()

```

**Step 2.** Server function

```{r server}
#| eval: false
server <- function(input, output) {}

```

**Step 3.** Statement to run shiny app

```{r shinyapp}
#| eval: false
shinyApp(ui = ui, server = server)

```

Alternatively, the `ui` and `server` functions can be organized in two script files, a `ui.R` and a `server.R` script, respectively. 

## Develop and test Shiny app locally

Open R and set session to parent directory (here `myappdir`) containing shiny script `app.R`, and the
run it with the `runApp()` function. A sample `app.R` script for testing can be downloaded from [here](https://raw.githubusercontent.com/tgirke/GEN242/refs/heads/main/tutorials/shinyapps/scripts/app.R).

```{r runshinyapp1}
#| eval: false
library(shiny)
dir.create("myappdir")
download.file("https://raw.githubusercontent.com/tgirke/GEN242/refs/heads/main/tutorials/shinyapps/scripts/app.R", "./myappdir/app.R")
runApp("myappdir") # To show code in app, add argument: display.mode="showcase" 

```

This will open the app in a web browser.

## Deploy on web server

This can be done on local or cloud systems. An easy solution is to get an account on [shinyapps.io](http://www.shinyapps.io/)
and then deploy Shiny apps there. For details, see [here](https://shiny.posit.co/r/articles/share/).

```{r deployshinyapp1}
#| eval: false
setwd("myappdir")
library(rsconnect)
deployApp()

```

## Example Shiny app

The following Shiny app is hosted on `shinyapps.io` (here Instructor account) and embedded into the markdown (or html) source of this page
using the following iframe syntax:

```html
<iframe src="https://tgirke.shinyapps.io/diamonds/" style="border: none; width: 880px; height: 900px"></iframe>
```

<iframe src="https://tgirke.shinyapps.io/diamonds/" style="border: none; width: 880px; height: 900px"></iframe>


Another example from Nick Harding using Shiny App: [volcanoshiny](https://github.com/hardingnj/volcanoshiny)

<iframe src="https://hardingnj.shinyapps.io/volcanoshiny/" style="border: none; width: 880px; height: 900px"></iframe>

Additional examples

   + Volcano Plots: [VolcaNoseR](https://huygens.science.uva.nl/VolcaNoseR/) ([publication](https://www.nature.com/articles/s41598-020-76603-3)).
   + systemPipeShiny: [web demo](https://tgirke.shinyapps.io/systemPipeShiny/) and [Bioc package](https://www.bioconductor.org/packages/release/bioc/html/systemPipeShiny.html)
   + spatialHeatmap: [web demo](https://spatialheatmap.org/) 

## Resources to Learn Shiny

### Built-in examples

The `shiny` package ships with example apps that are a good starting point. To explore them:

```{r learnshiny}
#| eval: false
mydir <- system.file("examples", package="shiny")
dir.create('my_shiny_test_dir')
file.copy(mydir, "my_shiny_test_dir", recursive=TRUE)
setwd("my_shiny_test_dir/examples")
runApp("01_hello") # Runs first example app in directory 
dir() # Lists available Shiny examples (directories). 

```

Individual examples can also be loaded directly — see [Lesson 1](https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/) on the Posit Shiny site.

### Tutorials and books

- Official Shiny [tutorial videos and articles](https://shiny.posit.co/r/getstarted/)
- Shiny [official gallery and source code](https://shiny.posit.co/r/gallery/)
- Advanced Shiny book — [Mastering Shiny](https://mastering-shiny.org/index.html)
- Advanced web application in R book — [Javascript for R](https://book.javascript-for-r.com/)

### Extension packages and tools

- Catalog of extension packages — [Awesome Shiny](https://github.com/nanxstats/awesome-shiny-extensions)
- [shinyWidgets](https://github.com/dreamRs/shinyWidgets) — UI components
- [systemPipeShiny](https://systempipe.org/sps/) — A framework for workflow management and data visualization
- [spsComps](https://systempipe.org/sps/dev/spscomps/) — UI components, animations, server components
- [shinyjs](https://deanattali.com/shinyjs/) — server-end JavaScript communications
- [shinylive](https://posit-dev.github.io/r-shinylive/) — Run Shiny apps entirely in the browser via WebAssembly (no server required); also embeddable directly in Quarto documents via `{shinylive-r}` chunks

## Session Info

```{r sessionInfo}
sessionInfo()

```

## References