inst/ShinySpaniel/app.R

In Spaniel: Spatial Transcriptomics Analysis

options(repos = BiocManager::repositories())
options(shiny.maxRequestSize=100*1024^2)

if(!require("shiny"))
    install.packages("shiny")
if(!require("dplyr"))
    install.packages("dplyr")
if(!require("ggplot2"))
    install.packages("ggplot2")
if (!require("devtools")) 
    install.packages("devtools")
if (!require("Seurat")) 
    devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0')
if (!require("Spaniel")) 
    devtools::install_github(repo = "RachelQueen1/Spaniel")

library(shiny)
library(Seurat)
library(Spaniel)
library(ggplot2)
library(dplyr)



############ ui #################################
ui <- pageWithSidebar(
    
    # App title ----
    headerPanel("Spatial Transcriptomics"),
    
    # Sidebar panel for inputs ----
    sidebarPanel(
        
        # Input: Select a file ----
        fileInput("dataFile", "Upload Data File",
                  multiple = FALSE,
                  accept = c(".rds")),
        
        # Title: Upload image file ----  
        fileInput("imageFile", "Upload Image File",
                  multiple = FALSE,
                  accept = c(".rds")),
        
        # Extra options for cluster or gene plots
        uiOutput("plotType"),
        
        # Input: for type of plot ----
        uiOutput("moreControls"), 
        
        p(
            #"Side End"
        )
        
    ),
    
    
    # Main panel for displaying outputs ----
    mainPanel(
        #plotOutput("plotPressed"), 
        
        tabsetPanel(id = "inTabset", 
                    type = "tabs",
                    tabPanel("Getting started",
                             value = "panel1",
                             h3("Plotting Spatial Data"),
                             p("1. Upload the data.rds file and image.rds 
                               files. It can take a couple of minutes for 
                               the data to upload"),
                             p("2. Select the type of plot you want to 
                               look at. There are 4 plots available showing 
                               a) the number of genes detected per spot, 
                               b) the number of reads detected per spot, 
                               c) clustering results,
                               d) the gene expression of a selected 
                               gene."),
                             p("3. For the cluster plot you must 
                               also select the cluster resolution you 
                               wish to plot
                               (generally a lower resolution equates to 
                               fewer clusters."),
                             p("4. For the gene plot you must select a gene 
                               from the drop downlist. There is a bit of a 
                               delay whilst the gene list is loading.
                               You can jump to the gene in list by typing the
                               first few letters of the gene of interest."), 
                             p("5. Click 'Plot' button in the side bar ")
                    ),
                    tabPanel(title = "View Plots",
                             value = "panel2",
                             plotOutput("plotPressed"))
                    
        )
    )    
)    



############ Server #################################

# Define server  ----
server <- function(input, output, session) {
    
    output$summary <- renderPrint({
        "1. Upload the data.rds file and image.rds files. 
        It can take a couple of minutes for the data to upload"
    })
    
    
    ### S4 object
    Object <- reactive({
        req(input$dataFile)
        readRDS(input$dataFile$datapath)
    })
    
    ### Image object
    imageObj <- reactive({
        req(input$imageFile)
        readRDS(input$imageFile$datapath)
    })
    
    ## Choose plot type
    ## if image and seurat objects uploaded 
    output$plotType <- renderUI({
        req(input$dataFile) 
        req(input$imageFile)
        radioButtons("Type_Of_Plot", "Type of plot:",
                     c("Gene Number Per Spot Plot" = "NoGenes",
                       "Counts Per Spot Plot" = "CountsPerSpot",
                       "Cluster Plot" = "Cluster",
                       "Gene Plot" = "Gene"
                     ))
        
    })
    
    #### Cluster list object TO ADD!!
    clusterList <- reactive({
        req(Object())
        metadata = getMetadata(Object())
        colnames(metadata)[grep("cluster_", colnames(metadata))]
    })
    
    ### Extra options for Gene or Cluster plots
    output$moreControls <- renderUI({
        if (req(input$Type_Of_Plot) == "Cluster") {
            list(selectInput("noClusters", "Select clustering resolution:", 
                             clusterList()),
                 actionButton("doPlot", "Plot")
            )
            
        }
        else if (req(input$Type_Of_Plot) == "Gene") {
            s = Object()
            geneList = rownames(s)
            list(selectInput("gene", "Select gene to plot:", 
                             geneList),
                 actionButton("doPlot", "Plot")
            )
        }
        else {
            actionButton("doPlot", "Plot")
        }
        
    })
    
    
    output$plotPressed = renderPlot({
        ## seurat object
        req(input$doPlot)
        s = Object()
        
        ##create coordinates df
        # coordinates = s@meta.data[, c("x", "y")]
        # coordinates$spot = rownames(coordinates)
        metadata = getMetadata(s)
        coordinates = getCoordinates(metadata)
        
        
        ## image grob
        g = imageObj()
        
        ## plot type
        pType = input$Type_Of_Plot
        
        ## set features (NULL for all plots except Gene)
        f = NULL
        if (input$Type_Of_Plot == "Gene"){
            f = input$gene
        }
        
        ## set clusters (NULL for all plots except Cluster)
        cl = NULL
        if (input$Type_Of_Plot == "Cluster"){
            cl = input$noClusters
        }
        
        ### create plot
        spanielPlot(Object = s, 
                Grob = g, 
                PlotType =  pType, 
                Gene = f, 
                ClusterRes = cl,
                CustomTitle = NULL, 
                ScaleData = TRUE)
    },
    
    
    height = 800, width = 800
    
    
    )
    
    observeEvent(input$doPlot, {
        updateTabsetPanel(session, "inTabset",
                          selected = "panel2"
        )
    })
    
    
}

shinyApp(ui, server)