Fc/shiny app

app_1/app.R

@@ -1,37 +1,106 @@
+library(shiny)
+library(shinythemes)
 
-library(maftools)
 
-endometrial_maf <- tcgaLoad(study= "UCEC")
+ui <- fluidPage(
+  shinythemes::themeSelector(),
+  navbarPage(
+    "ReproCanAtlas",
+    tabPanel("Start",
+             sidebarPanel(
+               textInput("tissue_type", "Tissue Type:", "Endometrial"),
+               textInput("project", "Project:", "UCEC"),
+               textInput("data_source", "Data Source:", "TCGA"),
+               sliderInput("alpha", "Alpha:", 0.001, 0.05, 0.05),
+               actionButton("analyze", "Analyze", class = "btn-primary")
+             ),
+             mainPanel(
+               tabsetPanel(
+                 tabPanel("DESeq Summary", verbatimTextOutput("deseq_summary")),
+                 tabPanel("MA Plot", plotOutput("maplot")),
+                 tabPanel("Counts", plotOutput("countplot")),
+                 tabPanel("Log2 Fold Change", plotOutput("lfcplot")),
+                 tabPanel("Mean SD", plotOutput("sdplot")),
+                 tabPanel("Groups", plotOutput("groupsplot"))
+               )
+             )
+    ),
+    tabPanel("Mutation Analysis", 
+             mainPanel(
+               tabsetPanel(
+                 tabPanel("MAF Summary", plotOutput("maf_summary")),
+                 tabPanel("Oncoplot", plotOutput("oncoplot")),
+                 tabPanel("Transition and Transversion Ratios", plotOutput("titv")),
+                 tabPanel("Amino Acid Changes", textInput("gene_input", label="Gene:", value="PTEN"), plotOutput("aa_lollipop")),
+                 tabPanel("Inter Variant Distance", plotOutput("ivd")),
+                 tabPanel("Somatic Interactions", plotOutput("somatic_interactions")),
+                 tabPanel("Oncodrive", plotOutput("oncodrive"))
+               )
+             )
+    )
+  )
+)
 
 
-# Define UI for app that draws a histogram ----
-ui <- fluidPage(
-  #Sidebar panel for inputs ----
-    sidebarPanel( 
-      checkboxGroupInput("Data", label = h3("Data Types to View"), choices = c("WXS", "RNAseq", "scRNAseq", "Cell Line"), selected = NULL)),
+server <- function(input, output) {
+  output$deseq_summary <- renderPrint({
+    summary(results(dds, alpha=input$alpha))
+  })
 
-      textInput("Gene of Interest","Gene of Interest for RNAseq"),
+  output$maplot <- renderPlot({
+    plotMA(res, ylim= c(-2,2))
+  })
 
+  output$countplot <- renderPlot({
+    plotCounts(dds, gene=which.min(res$padj), intgroup="condition")
+  })
 
-  # App title ----
-  titlePanel("ReproCanAtlas"),
-
-    # Main panel for displaying outputs ----
+  output$lfcplot <- renderPlot({
+    plotMA(resLFC, ylim= c(-2,2))
+  })
 
-  mainPanel(
-   plotOutput(outputId = "summary"),  
-    plotOutput(outputId = "oncoplot"))
-  )
-
-
-
-# Define server logic required to ----
-server <- function(input, output) {
-
-  output$summary <- renderPlot(plotmafSummary(maf = endometrial_maf, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE))   
+  output$sdplot <- renderPlot({
+    meanSdPlot(assay(ntd))
+  })
+
+  output$groupsplot <- renderPlot({
+    q
+  })
+
+  output$maf_summary <- renderPlot({
+    plotmafSummary(maf = endometrial_maf, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE)
+  })
+
+  output$oncoplot <- renderPlot({
+    oncoplot(maf = endometrial_maf, top = 10)
+  })
+
+  output$titv <- renderPlot({
+    plotTiTv(res = laml.titv)
+  })
+
+  output$ivd <- renderPlot({
+    rainfallPlot(maf = endometrial_maf, detectChangePoints = TRUE, pointSize = 0.4)
+  })
+
+  output$aa_lollipop <- renderPlot({
+    lollipopPlot(
+      maf = endometrial_maf,
+      gene = input$gene_input,
+      AACol = 'HGVSp_Short',
+      showMutationRate = TRUE
+    )
+  })
+
+  output$somatic_interactions <- renderPlot({
+    somaticInteractions(maf = endometrial_maf, top = 25, pvalue = c(0.05, 0.1))
+  })
+
+  output$oncodrive <- renderPlot({
+    plotOncodrive(res = laml.sig, fdrCutOff = 0.1, useFraction = TRUE, labelSize = 0.5)
+  })
 
-  output$oncoplot <- renderPlot(oncoplot(maf = endometrial_maf, top = 10))
-  } 
+} 
 
 
 shinyApp(ui = ui, server = server)

app_1/install.R

@@ -0,0 +1,12 @@
+if (!require("BiocManager", quietly = TRUE))
+  install.packages("BiocManager")
+
+BiocManager::install("recount3")
+BiocManager::install("tximport")
+BiocManager::install("GenomicFeatures")
+BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
+BiocManager::install("vsn")
+BiocManager::install("DESeq2")
+BiocManager::install("maftools")
+BiocManager::install("apeglm")
+install.packages("tidyverse")