slide_shiny2.Rmd

---
title: "R Shiny - Part II"
subtitle: "Workshop on Data Visualization in R"
author: "`r paste0('<b>Lokesh Mano</b> • ',format(Sys.time(), '%d-%b-%Y'))`"
institute: NBIS, SciLifeLab
keywords: bioinformatics, course, workshop, scilifelab, nbis
output:
  xaringan::moon_reader:
    encoding: 'UTF-8'
    self_contained: false
    chakra: 'assets/remark-latest.min.js'
    css: 'assets/slide.css'
    lib_dir: libs
    nature:
      ratio: '4:3'
      highlightLanguage: r
      highlightStyle: github
      highlightLines: true
      countIncrementalSlides: false
      slideNumberFormat: "%current%/%total%"
    include: NULL
---

exclude: true
count: false

```{r,echo=FALSE,child="assets/header-slide.Rmd"}
```

```{r,include=FALSE}
# load the packages you need
library(dplyr)
library(tidyr)
library(tidyverse)
#library(stringr)
library(ggplot2)
#library(plotly)
#library(pheatmap)
#library(DESeq2)
#library(edgeR)
library(kableExtra)
```

---

name: content
class: spaced

## Contents

* [Reactivity](#react)
* [Isolate reactivity](#isolate)
* [observeEvent()](#observe)
* [Updating Widgets](#updating)
* [Error Validation](#error)
* [Download Button](#download)
* [Modularizing reactivity](#module)

---

name: react

## Reactivity

.size-95[
<img src="assets/images/react-code1.png" alt="drawing" width="800"/>
]

---

name: react1

## Reactivity

.size-95[
<img src="assets/images/react-code2.png" alt="drawing" width="800"/>
]

---

name: react2

## Reactivity

.size-95[
<img src="assets/images/react-code3.png" alt="drawing" width="800"/>
]

---

name: react3

## Reactivity

.size-95[
<img src="assets/images/react-code4.png" alt="drawing" width="800"/>
]

---

name: react4

## Reactivity

.size-95[
<img src="assets/images/react5.png" alt="drawing" width="800"/>
]

---

name: react5

## Reactivity

.size-95[
<img src="assets/images/react6.png" alt="drawing" width="800"/>
]

---

name: isolate

## Isolate reactivity

* Reactivity can be controlled.

--

* You will notice that as soon as you try to change the title, the histogram will update with new values

.size-95[
<img src="assets/images/isolate1.png" alt="drawing" width="800"/>
]
---


name: isolate2

## Isolate reactivity

.size-95[
<img src="assets/images/isolate2.png" alt="drawing" width="800"/>
]
---

name: isolate3

## Isolate reactivity

.size-95[
<img src="assets/images/isolate3.png" alt="drawing" width="800"/>
]

---

name:isolate4

## Isolate reactivity

.size-95[
<img src="assets/images/isolate4.png" alt="drawing" width="800"/>
]

---

name:observe

## observeEvent()

.size-95[
<img src="assets/images/observe.png" alt="drawing" width="500"/>
]

---

name: updating

## Updating widgets

* Widgets can be updated once initialised.
* Add third argument **session** to server function

```
server=function(input,output,session) {}
```

--

* Example of a typical UI

```
ui=fluidPage(
  selectInput("select-input",label="selectInput",choices=c("A","B","C")),
  numericInput("numeric-input",label="numericInput",value=5,min=1,max=10),
  sliderInput("slider-input",label="sliderInput",value=5,min=1,max=10),
)
```

--

* Update functions can be used to update input widgets
* Reactive observer `observe({})` monitors for a conditional change

```
server=function(input,output,session) {
  observe({
    if(something) {
      updateSelectInput(session,"select-input",label="selectInput",choices=c("D","E","F"))
      updateNumericInput(session,"numeric-input",label="numericInput",value=10,min=1,max=10)
      updateSliderInput(session,"slider-input",label="sliderInput",value=8,min=1,max=10)
    }
  })
}
```

---

name: error

## Error validation

* Shiny returns an error with missing or incorrect values

.pull-left-70[.limity100[
```{r,eval=FALSE}
shinyApp(
ui=fluidPage(
  selectInput("data_input",label="Select data",
              choices=c("","mtcars","faithful","iris")),
  tableOutput("table_output")
),
server=function(input, output) {
  getdata <- reactive({ get(input$data_input,'package:datasets') })
  output$table_output <- renderTable({head(getdata())})
})
```
]]

.pull-right-30[
![](assets/images/val1.png)
]

--

* Errors can be handled in a controlled manner

--

* `validate()` can be used to check input
* `validate()` using `need()`

.pull-left-70[.limity100[
```
shinyApp(
ui=fluidPage(
  selectInput("data_input",label="Select data",
              choices=c("","mtcars","faithful","iris")),
  tableOutput("table_output")
),
server=function(input, output) {
  getdata <- reactive({ 
  validate(need(try(input$data_input),"Please select a data set"))
    get(input$data_input,'package:datasets') 
    })
  output$table_output <- renderTable({head(getdata())})
})
```
]]

.pull-right-30[
![](assets/images/val2.png)
]

--

* `validate()` using custom function

.pull-left-70[.limity100[
```
valfn <- function(x) if(is.null(x) | is.na(x) | x=="") return("Input data is incorrect.")
shinyApp(
ui=fluidPage(
  selectInput("data_input",label="Select data",
              choices=c("","mtcars","faithful","iris")),
  tableOutput("table_output")
),
server=function(input,output) {
  getdata <- reactive({ 
  validate(valfn(try(input$data_input)))
    get(input$data_input,'package:datasets')
    })
  output$table_output <- renderTable({head(getdata())})
})
```
]]

.pull-right-30[
![](assets/images/val3.png)
]

--

* `shiny::req()` checks input variable and silently stops execution

---

name: download

## Download • Data

* Add button and `downloadHandler()` function

```
shinyApp(
ui=fluidPage(
  selectInput("data_input",label="Select data",
              choices=c("mtcars","faithful","iris")),
  textOutput("text_output"),
  downloadButton("button_download","Download")
),
server=function(input, output) {
  getdata <- reactive({ get(input$data_input, 'package:datasets') })
  output$text_output <- renderText(paste0("Selected dataset: ",input$data_input))
  
  output$button_download <- downloadHandler(
  filename = function() {
     paste0(input$data_input,".csv")
   },
  content = function(file) {
     write.csv(getdata(),file,row.names=FALSE,quote=F)
   })
})
```

* Run in system browser if Rstudio browser doesn't work
* See usage of download buttons

---

name: download-plot

## Download • Plots

```
shinyApp(
ui=fluidPage(
  selectInput("data_input",label="Select data",
              choices=c("mtcars","faithful","iris")),
  textOutput("text_output"),
  plotOutput("plot_output",width="400px"),
  downloadButton("button_download", "Download")
),
server=function(input, output) {
  getdata <- reactive({ get(input$data_input, 'package:datasets') })
  output$text_output <- renderText(paste0("Selected dataset: ",input$data_input))
  output$plot_output <- renderPlot({hist(getdata()[, 1])})
  
output$button_download <- downloadHandler(
  filename = function() {
    paste0(input$data_input,".png")
  },
  content = function(file) {
    png(file)
    hist(getdata()[, 1])
    dev.off()
  })
})
```

* Run in system browser if Rstudio browser doesn't work
* See usage of download buttons

---


name: module

## Modularizing Reactivity

.size-95[
<img src="assets/images/shiny-mod.png" alt="drawing" width="800"/>
]

---


name: end_slide
class: end-slide, middle
count: false

# Thank you. Questions?

Slide courtesy: Roy Francis (NBIS, RaukR2021)

```{r,echo=FALSE,child="assets/footer-slide.Rmd"}
```

```{r,include=FALSE,eval=FALSE}
# manually run this to render this document to HTML
rmarkdown::render("slide_sample.Rmd")
# manually run this to convert HTML to PDF
#pagedown::chrome_print("slide_sample.html",output="slide_sample.pdf")
```