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146 lines
4.0 KiB
146 lines
4.0 KiB
library(shiny)
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library(Seurat)
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library(shinyFiles)
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library(ggplot2)
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library(ggpubr)
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# Define UI for application
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ui <- fluidPage(
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# Application title
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titlePanel("scMonitor"),
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sidebarLayout(
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sidebarPanel(
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shinyFilesButton("file", label="Select File", title="Select a Seurat Object", multiple=F),
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uiOutput('groupby'),
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uiOutput('facetby'),
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textInput('features', label = "Genes"),
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textInput('mods', label = "Signatures"),
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actionButton("goButton", "Query"),
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sliderInput("height", "Altura", min=1000, max=20000, step=1000, value=6000),
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h3("Add Signature"),
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textInput('mod_name', label = "Name"),
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textInput('mod_feat', label = "Genes"),
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actionButton("modButton", "Add Signature")
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),
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mainPanel(
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plotOutput("umapPlot"),
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uiOutput("featPlotUI")
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)
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)
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)
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# Define server logic
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server <- function(input, output) {
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## Defining reactive values
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dades<-reactiveValues()
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dades$seu<-NULL
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dades$mods<-NULL
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## Conecting with file location and entering Seurat object
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volumes <- c(Home = fs::path_home(), "R Installation" = R.home(), getVolumes()())
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shinyFileChoose(input, 'file', roots=volumes)
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observe({
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if (!is.integer(input$file)){
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dades$seu<-readRDS(parseFilePaths(volumes, input$file)$datapath)
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}
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})
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## Rendering UI depending on seu meta.data
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output$groupby<-renderUI({
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if (!is.null(dades$seu)){
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selectInput("groupby", "GroupBy", c("Default", colnames(dades$seu@meta.data)))
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}
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})
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output$facetby<-renderUI({
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if (!is.null(dades$seu)){
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selectInput("facetby", "FacetBy", c("None", colnames(dades$seu@meta.data)))
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}
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})
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## Render DimPlot
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output$umapPlot <- renderPlot({
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observeEvent(dades$seu, {})
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if (!is.null(dades$seu)){
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plot<-DimPlot(dades$seu,
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group.by = if(input$groupby != "Default"){input$groupby}else{NULL},
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split.by=if(input$facetby != "None"){input$facetby}else{NULL})+
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theme(aspect.ratio=1)
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plot
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}
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})
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## Signature - Module Definition
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observeEvent(input$modButton, {
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if (input$modButton > 0){
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mod_list<-strsplit(input$mod_feat, " ")[[1]]
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mod_list<-mod_list[mod_list %in% rownames(dades$seu)]
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dades$seu<-AddModuleScore(dades$seu,list(mod_list),
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name=input$mod_name)
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}
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})
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## FeaturePlot construction
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query<-eventReactive(input$goButton,{
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dades$fet_query<-strsplit(input$features, " ")[[1]]
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})
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output$featPlotUI<- renderUI({
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observeEvent(dades$fet_query, {})
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if (!is.null(dades$seu)){
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plotOutput("featPlot",
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height = paste0(input$height/10,"px"))
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}
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})
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## ModulePlot/SigPlot construction
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query_mod<-eventReactive(input$goButton,{
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if (length(strsplit(input$mods, " ")[[1]]) > 0){
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dades$mods<-paste(strsplit(input$mods, " ")[[1]], "1", sep="")
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}else{
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dades$mods<-NULL
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}
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})
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output$modPlotUI<- renderUI({
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observeEvent(dades$mod_name, {})
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if (!is.null(dades$mod_name)){
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plotOutput("modPlot",
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height = paste0(input$height/10,"px"))
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}
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})
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## Feature/Mod plot rendering
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output$featPlot<-renderPlot({
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observeEvent(input$goButton, {})
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if (!is.null(dades$seu)){
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query()
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plot<-list()
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print(dades$fet_query)
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if (length(dades$fet_query) > 0){
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plot[["Genes"]]<-FeaturePlot(dades$seu,
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split.by=if(input$facetby != "None"){input$facetby}else{NULL},
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features = dades$fet_query)&theme(aspect.ratio = 1)
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}
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query_mod()
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print(dades$mods)
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if (length(dades$mods) > 0){
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plot[["Mods"]]<-FeaturePlot(dades$seu,
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split.by=if(input$facetby != "None"){input$facetby}else{NULL},
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features = dades$mods)&theme(aspect.ratio = 1)&scale_color_viridis_c()
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}
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do.call(ggarrange, c(plot, ncol=1))
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}
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})
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}
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# Run the application
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shinyApp(ui = ui, server = server)
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