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mictes · Apr 9, 2024 · 97ab96b · 97ab96b
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+.DS_Store
diff --git a/R_Code/exercises/01_calculator.R b/R_Code/exercises/01_calculator.R
@@ -0,0 +1,39 @@
+library(shiny)
+
+# Define UI
+ui <- fluidPage(
+  titlePanel(""),
+
+  sidebarLayout(
+    sidebarPanel(
+      # input here
+      # check: https://shiny.posit.co/r/gallery/widgets/widget-gallery/
+    ),
+
+    mainPanel(
+     # output here
+     # check: https://github.com/rstudio/cheatsheets/blob/main/shiny.pdf
+    )
+  )
+)
+
+# Define server logic
+server <- function(input, output) {
+
+  output$result <- renderText({
+    num1 <- 2
+    num2 <- 1
+
+    result <- switch(input$operation,
+           "add"      = num1 + num2,
+           "subtract" = num1 - num2,
+           "multiply" = num1 * num2,
+           "divide"   = num1 / num2
+    )
+
+    paste("Result:", result)
+  })
+}
+
+# Run the application
+shinyApp(ui = ui, server = server)
diff --git a/R_Code/misc/k_means_reactlog.R b/R_Code/misc/k_means_reactlog.R
@@ -0,0 +1,55 @@
+library(shiny)
+library(reactlog)
+
+reactlog_enable()
+
+ui <- function() {
+
+  # k-means only works with numerical variables,
+  # so don't give the user the option to select
+  # a categorical variable
+  vars <- setdiff(names(iris), "Species")
+
+pageWithSidebar(
+  headerPanel('Iris k-means clustering'),
+  sidebarPanel(
+    selectInput('xcol', 'X Variable', vars),
+    selectInput('ycol', 'Y Variable', vars, selected = vars[[2]]),
+    numericInput('clusters', 'Cluster count', 3, min = 1, max = 9)
+  ),
+  mainPanel(
+    plotOutput('plot1')
+  )
+)}
+
+
+
+
+server <- function(input, output, session) {
+
+    # Combine the selected variables into a new data frame
+    selectedData <- reactive({
+      iris[, c(input$xcol, input$ycol)]
+    })
+
+    clusters <- reactive({
+      kmeans(selectedData(), input$clusters)
+    })
+
+    output$plot1 <- renderPlot({
+      palette(c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3",
+                "#FF7F00", "#FFFF33", "#A65628", "#F781BF", "#999999"))
+
+      par(mar = c(5.1, 4.1, 0, 1))
+      plot(selectedData(),
+           col = clusters()$cluster,
+           pch = 20, cex = 3)
+      points(clusters()$centers, pch = 4, cex = 4, lwd = 4)
+    })
+
+}
+
+shinyApp(ui = ui, server = server)
+
+shiny::reactlogShow()
+
diff --git a/R_Code/solutions/01_calculator.R b/R_Code/solutions/01_calculator.R
@@ -0,0 +1,46 @@
+library(shiny)
+
+# Define UI
+ui <- fluidPage(
+  titlePanel("Shiny Calculator"),
+
+  sidebarLayout(
+    sidebarPanel(
+      numericInput("num1", label = "Enter first number:", value = 0),
+      numericInput("num2", label = "Enter second number:", value = 0),
+      radioButtons("operation", label = "Choose operation:", choices = list(
+        "Add"      = "add",
+        "Subtract" = "subtract",
+        "Multiply" = "multiply",
+        "Divide"   = "divide"
+      ))
+    ),
+
+    mainPanel(
+      textOutput("result")
+    )
+  )
+)
+
+# Define server logic
+server <- function(input, output) {
+
+  output$result <- renderText({
+    if (input$operation == "divide") {
+      req(input$num2 != 0)
+    }
+
+    result <- switch(input$operation,
+                     "add"      = input$num1 + input$num2,
+                     "subtract" = input$num1 - input$num2,
+                     "multiply" = input$num1 * input$num2,
+                     "divide"   = input$num1 / input$num2
+    )
+
+    paste("Result:", result)
+  })
+
+}
+
+# Run the application
+shinyApp(ui = ui, server = server)
diff --git a/R_Code/solutions/01_calculator_reactive.R b/R_Code/solutions/01_calculator_reactive.R
@@ -0,0 +1,51 @@
+library(shiny)
+
+# Define UI
+ui <- fluidPage(
+  titlePanel("Shiny Calculator"),
+
+  sidebarLayout(
+    sidebarPanel(
+      numericInput("num1", "Enter first number:", value = 0),
+      numericInput("num2", "Enter second number:", value = 0),
+      radioButtons("operation", "Choose operation:",
+                   choices = list("Add" = "add",
+                                  "Subtract" = "subtract",
+                                  "Multiply" = "multiply",
+                                  "Divide" = "divide"))
+    ),
+
+    mainPanel(
+      textOutput("result")
+    )
+  )
+)
+
+# Define server logic
+server <- function(input, output) {
+
+  result <- reactive({
+    # Handling division by zero with req()
+    if (input$operation == "divide") {
+      req(input$num2 != 0)
+    }
+
+    switch(input$operation,
+           "add"      = input$num1 + input$num2,
+           "subtract" = input$num1 - input$num2,
+           "multiply" = input$num1 * input$num2,
+           "divide"   = input$num1 / input$num2
+    )
+  })
+
+  print(input$num1)
+  # print(result())
+
+  output$result <- renderText({
+    paste("Result:", result())
+  })
+
+}
+
+# Run the application
+shinyApp(ui = ui, server = server)
diff --git a/Slides/01_Introduction.html b/Slides/01_Introduction.html
@@ -459,7 +459,7 @@ <h2>Output Rendering functions</h2>
 					<h2 class="highlight">Exercise 1</h2>
 					<p><strong>Resources:</strong></p>
 					<ul>
-						<li class="fragment">Exercises/<a href="../Exercises/1_calculator.R">1_calculator.R</a></li>
+						<li class="fragment">Exercises/<a href="../R_Code/exercises/01_calculator.R">1_calculator.R</a></li>
 						<li class="fragment">Input widgets: <a href="https://shiny.posit.co/r/gallery/widgets/widget-gallery/" target="_blank">Shiny widget gallery</a></li>
 						<li class="fragment">Render functions: <a href="https://github.com/rstudio/cheatsheets/blob/main/shiny.pdf" target="_blank">Shiny CHEATSHEET</a></li>
 					</ul>
@@ -1170,7 +1170,7 @@ <h2>Best practices</h2>
 						<li class="fragment">This also helps to avoid the accidental creation of loops</li>
 						<li class="fragment">Use <span class="highlight">req()</span> to avoid errors due to missing inputs, especially when opening the application</li>
 						<li class="fragment">Carefully check the IDs of the inputs and outputs</li>
-						<li class="fragment">Troubleshooting: use the <a href="../Misc/k_means_reactlog.R">library(reactlog)</a></li>
+						<li class="fragment">Troubleshooting: use the <a href="../R_Code/misc/k_means_reactlog.R">library(reactlog)</a></li>
 						<li class="fragment">Modularise, i.e. store ui and server as variables. This for example allows you to dynamically load parts of the UI later.</li>
 					</ul>
 				</section>

diff --git a/Slides/02_ggplot.html b/Slides/02_ggplot.html
@@ -33,7 +33,7 @@
 		<div class="reveal">
 			<div class="slides">
 
-				<section class="title">
+				<section class="title" data-menu-title="ggplot2 recap">
 					<h1 class="shiny">Interactive Data Visualization with R Shiny for Life Sciences</h1>
 					<h2>Day 1: ggplot2 recap</h2>
 					<strong>Michael Teske &amp; Jonas Schmid, Zurich 08 April 2024</strong>
@@ -228,7 +228,7 @@ <h3>Resources</h3>
 					</div>
 				</section>
 
-				<section data-auto-animate>
+				<section data-auto-animate data-menu-title="Violin plot">
 					<h2>Let's create a plot!</h2>
 					<div class="panel" style="width: 45%;">
 						<img src="materials/images/Iris_violin_point.png" alt="Iris_ViolinPlot" data-id="Iris_plot" width="600">
@@ -274,7 +274,7 @@ <h2>Let's create a plot!</h2>
 					</div>
 				</section>
 
-				<section data-auto-animate>
+				<section data-auto-animate data-menu-title="Volcano plot">
 					<h2>Let's create a plot! - Variant 2</h2>
 					<div class="panel" style="width: 45%;">
 						<img src="materials/images/Ruhland2016_volcano.png" alt="Ruhland2016_VolcanoPlot" data-id="Ruhland2016_plot" width="700">
@@ -321,7 +321,7 @@ <h2>Let's create a plot! - Variant 2</h2>
 					<h2>Questions?</h2>
 				</section>
 
-				<section>
+				<section data-menu-title="Exercise 2">
 					<h2 class="highlight">Exercise 2</h2>
 					<p><strong>Task:</strong> Create a plot with ggplot2!</p>
 					<div class="panel" style="width: 25%;">
@@ -358,7 +358,7 @@ <h2 class="highlight">Exercise 2</h2>
 									# Load data
 									ruhland2016 &lt;- read.csv('Ruhland2016.csv', row.names=1)
 
-									# Mark differentially expressed genes - HINT: Wrap this part in a reactive({})!
+									# Mark differentially expressed genes - Wrap this part in a reactive({})
 									log2FCthreshold &lt;- log2(1.5)
 									p_threshold     &lt;- 0.05
 

diff --git a/Slides/code/exercises/1_calculator.R b/Slides/code/exercises/1_calculator.R
@@ -0,0 +1,39 @@
+library(shiny)
+
+# Define UI
+ui <- fluidPage(
+  titlePanel(""),
+
+  sidebarLayout(
+    sidebarPanel(
+      # input here
+      # check: https://shiny.posit.co/r/gallery/widgets/widget-gallery/
+    ),
+
+    mainPanel(
+     # output here
+     # check: https://github.com/rstudio/cheatsheets/blob/main/shiny.pdf
+    )
+  )
+)
+
+# Define server logic
+server <- function(input, output) {
+
+  output$result <- renderText({
+    num1 <- 2
+    num2 <- 1
+
+    result <- switch(input$operation,
+           "add"      = num1 + num2,
+           "subtract" = num1 - num2,
+           "multiply" = num1 * num2,
+           "divide"   = num1 / num2
+    )
+
+    paste("Result:", result)
+  })
+}
+
+# Run the application
+shinyApp(ui = ui, server = server)
diff --git a/Slides/code/exercises/solutions/1_calculator.R b/Slides/code/exercises/solutions/1_calculator.R
@@ -0,0 +1,46 @@
+library(shiny)
+
+# Define UI
+ui <- fluidPage(
+  titlePanel("Shiny Calculator"),
+
+  sidebarLayout(
+    sidebarPanel(
+      numericInput("num1", label = "Enter first number:", value = 0),
+      numericInput("num2", label = "Enter second number:", value = 0),
+      radioButtons("operation", label = "Choose operation:", choices = list(
+        "Add"      = "add",
+        "Subtract" = "subtract",
+        "Multiply" = "multiply",
+        "Divide"   = "divide"
+      ))
+    ),
+
+    mainPanel(
+      textOutput("result")
+    )
+  )
+)
+
+# Define server logic
+server <- function(input, output) {
+
+  output$result <- renderText({
+    if (input$operation == "divide") {
+      req(input$num2 != 0)
+    }
+
+    result <- switch(input$operation,
+                     "add"      = input$num1 + input$num2,
+                     "subtract" = input$num1 - input$num2,
+                     "multiply" = input$num1 * input$num2,
+                     "divide"   = input$num1 / input$num2
+    )
+
+    paste("Result:", result)
+  })
+
+}
+
+# Run the application
+shinyApp(ui = ui, server = server)