Browse code

added shinytest

pablo-rodr-bio2 authored on 23/04/2021 10:14:15
Showing7 changed files

... ...
@@ -7,7 +7,7 @@ geneSetsUI <- function(id){
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     conditionalPanel(
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       condition = "input.genesetSourceType == 'fileGeneset'", ns = ns,
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       fileInput(ns("genesetFile"), "Choose GeneSet file:",
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-                accept = ".gmt")
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+                accept = c(".gmt", "text/csv", ".csv"))
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     ),
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     conditionalPanel(
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       condition = "input.genesetSourceType == 'varGeneset'", ns = ns, 
... ...
@@ -22,7 +22,12 @@ geneSetsServer <- function(id){
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     geneSets <- reactive({
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       if(input$genesetSourceType == "fileGeneset"){
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         if(is.null(input$genesetFile)) return(NULL) #this is in order to disable "run" btn
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-        genesets <- getGmt(input$genesetFile$datapath)
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+        ext <- tools::file_ext(input$genesetFile$name)
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+        genesets <- 
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+          switch(ext,
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+                 csv = as.list(read.csv(input$genesetFile$datapath)),
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+                 gmt = getGmt(input$genesetFile$datapath)
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+        )
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       } else {
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         if(is.null(input$genesetVar)) return(NULL)
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         genesets <- get(input$genesetVar)
... ...
@@ -4,143 +4,9 @@ function(input, output, session) {
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   rout <- tempfile("consoleText", fileext = ".txt")
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   file.create(rout)
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   console.text <- reactiveFileReader(200, session, rout, readLines, warn=F)
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-<<<<<<< HEAD
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-  
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-  # ERRORS MESSAGES
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-  output$errorsGsva <- renderText({
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-    req(argInp$varMinsz(), argInp$varMaxsz(), argInp$selectedTau())
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-    rv$errors.gsva
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-  })
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-
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-  # ENABLING 'RUN' BTN
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-  observe({
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-    if(!is.null(matrix()) && !is.null(genesets())){
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-      enable("button")
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-    } else {
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-      disable("button")
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-    }
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-  })
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-  
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-  ### INPUTS ###
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-  
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-  # DATA MATRIX
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-  matrix <- matrixServer("matrix1")
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-  
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-  # GENES
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-  genesets <- geneSetsServer("genes1")
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-  
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-  # ARGUMENTS
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-  argInp <- argumentsDataServer("argumentsInput")
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-  
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-
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-  #### GSVA RESULTS ####
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-  
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-  ## REACTIVE VALUES
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-  rv <- reactiveValues(gs=NULL, dat.t=NULL, n=NULL, dd.col=NULL, p=NULL, 
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-                       p2=NULL, p3=NULL, errors.gsva = NULL, sample.c = NULL)
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-  gsva.cancel <- reactiveVal(FALSE)
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-  
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-  ## GSVA RESULT
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-  observeEvent( input$button, {
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-    
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-    ## This js is in order to reset the event_data from the plotlys,
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-    ## so every time the .user hits the 'run' button, plotlys get back to null
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-    runjs("Shiny.setInputValue('plotly_click-click1', null);")
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-    runjs("Shiny.setInputValue('plotly_click-click2', null);")
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-    
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-    ## here we reset all the reactiveValues to NULL
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-    rv$gs <- NULL
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-    rv$dat.t <- NULL
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-    rv$p <- NULL
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-    rv$p2 <- NULL
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-    rv$p3 <- NULL
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-    rv$sample.c <- NULL
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-    rv$errors.gsva <- NULL
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-    
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-    ## this is a flag for the future. Futures cannot be canceled or
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-    ## terminated in a strict way, so when they get interrupted they
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-    ## throw an error that is not related to gsva(). When future is 
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-    ## interrupted, the flag goes TRUE in order to make the errors
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-    ## message print NULL
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-    gsva.cancel(FALSE)
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-    
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-    modalGSVAUI("modal.text")
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-    
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-    ## future() cannot take reactive values, so we must isolate() them
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-    future({
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-      ## sink() will redirect all console cats and prints to a
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-      ## text file that the main session will be reading in order
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-      ## to print the progress bar from bplaply()
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-      sink(rout)
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-      result <- gsva(isolate(matrix()),
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-                     isolate(genesets()), 
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-                     method=isolate(argInp$method()),
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-                     kcdf=isolate(argInp$kcdf()),
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-                     abs.ranking=isolate(argInp$absRanking()),
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-                     min.sz= isolate(argInp$varMinsz()),
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-                     max.sz=isolate(argInp$varMaxsz()),
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-                     parallel.sz=1L, ## by now, disable parallelism
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-                     mx.diff=isolate(argInp$mxDiff()),
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-                     tau=isolate(argInp$selectedTau()),
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-                     ssgsea.norm=isolate(argInp$ssgseaNorm()),
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-                     verbose=TRUE)
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-      sink()
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-      ## when gsva() ends, we reset the console text file to empty
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-      write("", file=rout)
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-      return(result)
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-    }, seed = TRUE) %...>%
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-      (function(result){
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-        ## the future's result will be the gsva() result, and we save it
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-        ## and transform it in reactiveValues(). In order to make the future
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-        ## not block the app at an inner-session level, we save the results in
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-        ## reactiveValues() and then at the end of the observeEvent() we return NULL
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-        ## in order to make the plots.
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-        ## https://github.com/rstudio/promises/issues/23#issuecomment-386687705
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-        rv$gs <- result
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-        rv$dat.t <- melt(as.data.table(rv$gs, keep.rownames = "gene.sets"),
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-                         variable.name = "Sample", id.vars="gene.sets")
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-        rv$n <- length(levels(rv$dat.t$Sample))
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-        rv$dd.col <- hcl(h = seq(15, 375, length=rv$n), l = 65, c = 100)[1:rv$n]
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-        names(rv$dd.col)  <- levels(rv$dat.t$Sample)
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-        
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-        ## finally, we leave the console.text file empty again and
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-        ## remove the modal
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-        write("", file=rout)
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-        removeModal()
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-      }) %...!%
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-      (function(error){
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-        ## there can be two ways to get an error here: 
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-        ## 1. gsva() fails, which is an ok error and should be returnet to user
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-        ## 2. User interrupts the future, which shouldn't be printed, that's
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-        ## why I use a flag to identify if error comes from pressing "Cancel" btn
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-        ## on the modal
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-        removeModal()
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-        write("", file=rout)
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-        if(gsva.cancel()){
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-          rv$errors.gsva <- NULL
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-        } else {
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-          rv$errors.gsva <- as.character(error)
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-        }
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-        
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-      })
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-    NULL
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-  })
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-  
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-  # PRINTING CONSOLE.TEXT
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-  modalGSVAServer("modal.text", console.text, gsva.cancel, rout)
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-  
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-  # PLOT1 RENDER
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-  plot1_Server("plot1", rv)
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-
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-  # PLOT2 RENDER
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-  eventData1 <- reactive({
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-    req(rv$dat.t)
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-    ind <- event_data("plotly_click", source = "click1")
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-    ind <- ind$curveNumber+1
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-=======
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-  ##################### INPUTS #####################
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+  ##################### INPUTS  ##################### 
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   # DATA MATRIX
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   matrix <- matrixServer("matrix1")
... ...
@@ -151,9 +17,8 @@ function(input, output, session) {
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   # ARGUMENTS
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   argInp <- argumentsDataServer("argumentsInput")
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-  
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-  ##################### GSVA RESULTS ################
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+  ##################### GSVA RESULTS  ##################### 
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   ## REACTIVE VALUES
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   rv <- reactiveValues(gs=NULL, dat.t=NULL, n=NULL, dd.col=NULL, p=NULL, 
... ...
@@ -244,47 +109,12 @@ function(input, output, session) {
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       })
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     NULL
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->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d
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   })
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-  plot2_Server("plot2", eventData1, rv)
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-  
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-<<<<<<< HEAD
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-  # PLOT3 RENDER
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-  eventData2 <- reactive({
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-    req(rv$p2)
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-    ind <- event_data("plotly_click", source = "click2")
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-    ind <- ind$pointNumber+1
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-  })
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-  plot3_Server("plot3", eventData2, rv, matrix, genesets)
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-  
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-  # DWN BTN
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-  downloadServer("download", reactive(rv$gs))
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-  
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-  # CLOSE BTN
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-  closeBtnServer("close", reactive(rv$gs))
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-
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-  
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-  # TEXT1
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-  output$text1 <- renderUI({
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-    req(rv$gs)
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-    HTML(paste("<br/>", "\t To see the Empirical Cumulative Distribution Function 
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-    of a Sample, click on its line in this plot and go
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-      to the 'Gene.Set' Panel", "<br/>", sep="<br/>"))
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-  })
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-  
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-  # TABLE
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-  output$result <- renderTable({
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-    req(rv$gs)
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-    resultInformation <- data.frame("Nr of gene sets" = nrow(rv$gs),
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-                                    "Nr of samples" = ncol(rv$gs))
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-    resultInformation
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-=======
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   # PRINTING CONSOLE.TEXT
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   modalGSVAServer("modal.text", console.text, gsva.cancel, rout)
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-  
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   ##################### OUTPUTS ##################
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   # PLOT1 RENDER
... ...
@@ -295,46 +125,29 @@ function(input, output, session) {
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     req(rv$dat.t)
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     ind <- event_data("plotly_click", source = "click1")
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     ind <- ind$curveNumber+1
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->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d
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+
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   })
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   plot2_Server("plot2", eventData1, rv)
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-  
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-<<<<<<< HEAD
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-  # TEXT2
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-  output$text2 <- renderUI({
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-    title1 <- rv$sample.c
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-    h2(tags$b(title1), align ="center")
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-=======
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+
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   # PLOT3 RENDER
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   eventData2 <- reactive({
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     req(rv$p2)
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     ind <- event_data("plotly_click", source = "click2")
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     ind <- ind$pointNumber+1
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->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d
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+
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   })
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   plot3_Server("plot3", eventData2, rv, matrix, genesets)
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-  
317
-<<<<<<< HEAD
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-  # TEXT3
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-  output$text3 <- renderUI({
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-    HTML(paste("<br/>", "\t To see the Kernel Density Estimation of genes of 
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-    any given Gene Set in this Sample,  click on any point in this plot and a
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-    second plot will appear bellow it", "<br/>", sep="<br/>"))
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-=======
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+
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   # ERRORS MESSAGES
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   output$errorsGsva <- renderText({
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     req(argInp$varMinsz(), argInp$varMaxsz(), argInp$selectedTau())
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     rv$errors.gsva
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->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d
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   })
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   # SESSION INFO
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   output$sessionInfo <- renderPrint({
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     sessionInfo()
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   })
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-<<<<<<< HEAD
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-
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-=======
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   ##################### UI SETUPS #####################
... ...
@@ -393,6 +206,4 @@ function(input, output, session) {
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     second plot will appear bellow it", "<br/>", sep="<br/>"))
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   })
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-
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->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d
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 }
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new file mode 100644
... ...
@@ -0,0 +1,3 @@
1
+library(shinytest)
2
+shinytest::testApp("../")
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+
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new file mode 100644
... ...
@@ -0,0 +1,22 @@
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0 23
new file mode 100644
... ...
@@ -0,0 +1,101 @@
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+"g93",0.238731735111441,0.0945835281735714,1.14526311038036,0.884250820028209,1.29408390614558,0.840539826961,1.19160126851033,0.886749037096059,-1.11641641193354,0.454577809057738,0.572811529859585,2.19359006906425,-0.0384567937093384,1.05724021270968,-0.786235919994713,-0.451812936257225,-1.25142446891953,1.56581433705846,1.14625997326498,0.246799211870998,-1.04384462163877,-0.350786392406381,1.63006733460683,0.730815610006591,-0.593948909367117,2.15647760195008,-0.562776208352765,-0.0584290512452095,-1.33826589318506,-0.491443047401821
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+"g94",-0.627906076039371,-0.895363357977542,-0.577468001059557,-0.829477611624518,-1.08999187241124,-0.285845423591384,-0.78896321811123,0.333369970155182,1.82853045813536,-0.213307143233068,1.01724924908461,0.156595323350149,1.49318484062772,1.27907258320933,2.2841164802616,-1.13662618777767,1.76454599657549,-1.03480801098526,-0.242583267705004,-0.73677153935145,-0.468696015002214,0.391720547858095,-0.480485227044419,0.545635528242466,1.07806733795125,0.702009423048609,-0.696955708518244,0.0906116207122605,-0.921029235202948,0.144417271262889
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+"g99",-0.235700359100477,-0.611165916680421,0.0209835863542375,-1.26068287881878,0.364114687355063,1.18118089143852,0.420574188698147,0.23111493441816,0.371147959759657,-0.522616697195916,0.484099387952522,-0.806482655703046,-0.0517182128948834,0.167940980736459,1.08911201091924,-2.24869006681656,0.0872442066052375,0.449936787146205,-0.280740054504004,0.536856022231548,0.741194719519762,0.165903101579443,-0.648299296516002,1.38051749338936,1.45128094388337,-1.44068097826971,-0.405540381007554,0.171301431637089,1.45390062123435,1.18901180052985
101
+"g100",-1.02642090030678,-1.18548008459731,1.24991457096922,-0.354542403073978,0.552157714218558,1.85991086154316,-1.61403945661912,0.647513357977592,0.2435327187603,-0.249190677755399,-0.244883779092525,0.372911595208748,0.908447698792251,-0.56610933289597,-0.163128989885215,0.838219387278491,0.0109618427990058,-1.03116449189746,0.734098736497243,-0.460485565976711,0.226852003567295,0.70533455324418,0.071960844365645,0.872634566795338,0.641551431409249,0.74047345310968,-0.743938496851104,-0.317376455269396,-0.864556217319535,0.834294073061504
0 102
new file mode 100644
... ...
@@ -0,0 +1,9 @@
1
+app <- ShinyDriver$new("../../", loadTimeout = 1e+05)
2
+app$snapshotInit("mytest1")
3
+
4
+app$uploadFile(`matrix1-matrixFile` = "matrix.csv")
5
+app$uploadFile(`genes1-genesetFile` = "genes.csv")
6
+app$setInputs(button = "click")
7
+app$setInputs(`modal.text-cancel` = "click")
8
+app$setInputs(Panels = "GeneSets")
9
+app$snapshot()
... ...
@@ -33,11 +33,7 @@ fluidPage(
33 33
       ))
34 34
     ),
35 35
     mainPanel(width=6,
36
-<<<<<<< HEAD
37
-              tabsetPanel(type="tabs",
38
-=======
39 36
               tabsetPanel(id = "Panels", type="tabs",
40
->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d
41 37
                           tabPanel("Samples",
42 38
                                    textOutput("errorsGsva"),
43 39
                                    htmlOutput("text1"),
... ...
@@ -45,11 +41,7 @@ fluidPage(
45 41
                                    tableOutput("result"),
46 42
                                    downloadUI("download"),
47 43
                                    closeBtnUI("close")),
48
-<<<<<<< HEAD
49
-                          tabPanel("Gene Sets",
50
-=======
51 44
                           tabPanel("GeneSets",
52
->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d
53 45
                                    uiOutput("text2"),
54 46
                                    htmlOutput("text3"),
55 47
                                    plot2_UI("plot2"),