diff --git a/inst/workflow/PipelineProtein/R/PipelineProtein_Normalization.R b/inst/workflow/PipelineProtein/R/PipelineProtein_Normalization.R index c84bc33..e0640f8 100644 --- a/inst/workflow/PipelineProtein/R/PipelineProtein_Normalization.R +++ b/inst/workflow/PipelineProtein/R/PipelineProtein_Normalization.R @@ -89,7 +89,7 @@ PipelineProtein_Normalization_server <- function(id, rv.custom.default.values <- list( tmp.dataset = NULL, - init.dataset = NULL, + #init.dataset = NULL, history = NULL, selectProt = reactive({NULL}) ) @@ -109,8 +109,32 @@ PipelineProtein_Normalization_server <- function(id, rv.custom.names = names(rv.custom.default.values) ) + # name <- id + # w.names <- names(widgets.default.values) + # rv.custom.names <- names(rv.custom.default.values) + # + # add.code <- "rv$dataIn <- NULL + # rv.custom$tmpAssay <- NULL" + # + # core.code <- paste0( + # Insert_Call_to_Config(name), + # Get_Code_Declare_widgets(w.names), + # #Get_Code_Update_Config_Variable(), + # Get_Code_for_ObserveEvent_widgets(w.names), + # Get_Code_for_rv_reactiveValues(), + # Get_Code_Declare_rv_custom(rv.custom.names), + # Get_Code_for_dataOut(), + # Get_Code_for_General_observeEvents(), + # Get_Code_for_remoteReset2_observeEvents(add.code), + # sep = "\n" + # ) + + + eval(str2expression(core.code)) + + # >>> # >>> START ------------- Code for Description UI--------------- # >>> @@ -162,7 +186,7 @@ PipelineProtein_Normalization_server <- function(id, observeEvent(input$Description_btn_validate, { rv$dataIn <- dataIn() - rv.custom$init.dataset <- dataIn() + #rv.custom$init.dataset <- dataIn() dataOut$trigger <- MagellanNTK::Timestamp() dataOut$value <- rv$dataIn @@ -193,7 +217,6 @@ PipelineProtein_Normalization_server <- function(id, tagList( - div(style = .style, uiOutput(ns("Normalization_btn_validate_ui")) ), @@ -256,28 +279,37 @@ PipelineProtein_Normalization_server <- function(id, # req(rv$dataIn) # remoteReset() # rv.custom$selectProt()$value - omXplore::omXplore_density_server("densityPlot_Norm", - obj = reactive({rv$dataIn}), - i = reactive({length(rv$dataIn)}) - ) - + # omXplore::omXplore_density_server("densityPlot_Norm", + # obj = reactive({rv$dataIn}), + # i = reactive({length(rv$dataIn)}) + # ) + # - observe({ - rv.custom$selectProt() - rv$dataIn + #observe({ + #selectProt() + # req(rv$dataIn) + - omXplore::omXplore_intensity_server("boxPlot_Norm", + # print("in toto") + + #print(rv$dataIn) + omXplore::omXplore_intensity_server("boxPlot_Norm", + obj = reactive({rv$dataIn}), + i = reactive({length(rv$dataIn)}), + track.indices = reactive({selectProt()$indices}), + remoteReset = reactive({remoteReset()}), + is.enabled = reactive({!rv$steps.enabled['Normalization']}) + ) + + omXplore::omXplore_density_server("densityPlot_Norm", obj = reactive({rv$dataIn}), - i = reactive({length(rv$dataIn)}), - track.indices = reactive({selectProt()$indices}), - remoteReset = reactive({remoteReset()}), - is.enabled = reactive({!rv$steps.enabled['Normalization']}) + i = reactive({length(rv$dataIn)}) ) - }) + #}) - observeEvent(rv.custom$selectProt()$indices, ignoreNULL = FALSE,{ + observeEvent(selectProt()$indices, ignoreNULL = FALSE,{ print("in observeEvent(selectProt()$indices") print('new value fo selectProt()$indices = ') @@ -292,7 +324,7 @@ PipelineProtein_Normalization_server <- function(id, widget <- selectInput( ns('Normalization_method'), "Normalization method", - choices = DaparToolshed::normalizeMethods(), + choices = setNames(nm = c("None", DaparToolshed::normalizeMethods())), selected = rv.widgets$Normalization_method, width = '250px') MagellanNTK::toggleWidget(widget, rv$steps.enabled['Normalization'] ) @@ -364,30 +396,33 @@ PipelineProtein_Normalization_server <- function(id, output$viewComparisonNorm_hc <- highcharter::renderHighchart({ req(rv$dataIn) req(length(rv$dataIn) > 1) + #req(names(rv$dataIn)[length(rv$dataIn)] == 'Normalization') obj1 <- rv$dataIn[[length(rv$dataIn)]] obj2 <- rv$dataIn[[length(rv$dataIn)-1]] req(obj1) req(obj2) protId <- omXplore::get_colID(rv$dataIn[[length(rv$dataIn)]]) - #browser() + + if (!is.null(selectProt()$indices)) { + .n <- length(selectProt()$indices) + .subset <- selectProt()$indices + } else { + .n <- floor(0.02 * nrow(obj1)) + .subset <- seq(nrow(obj1)) + } + + + DaparToolshed::compareNormalizationD_HC( - qDataBefore = SummarizedExperiment::assay(obj1), - qDataAfter = SummarizedExperiment::assay(obj2), + qDataBefore = SummarizedExperiment::assay(rv$dataIn, length(rv$dataIn)), + qDataAfter = SummarizedExperiment::assay(rv$dataIn, length(rv$dataIn)-1), keyId = rowData(rv$dataIn[[length(rv$dataIn)]])[, protId], conds = omXplore::get_group(rv$dataIn), pal = NULL, # Consider only 2% of the entire dataset - n = if (!is.null(rv.custom$selectProt()$indices)) { - length(selectProt()$indices) - } else { - floor(0.02 * nrow(SummarizedExperiment::assay(obj1))) - }, - subset.view = if (!is.null(selectProt()$indices)) { - selectProt()$indices - } else { - seq(nrow(obj1)) - } + n = .n, + subset.view = .subset ) }) @@ -447,6 +482,8 @@ PipelineProtein_Normalization_server <- function(id, # >>> END: Definition of the widgets observeEvent(input$Normalization_btn_validate, { + #browser() + # Do some stuff req(rv.widgets$Normalization_method) req(rv$dataIn) @@ -455,9 +492,8 @@ PipelineProtein_Normalization_server <- function(id, rv.custom$tmpAssay <- NULL try({ .conds <- colData(rv$dataIn)[, "Condition"] - qdata <- SummarizedExperiment::assay(rv$dataIn[[length(rv$dataIn)]]) + qdata <- SummarizedExperiment::assay(rv$dataIn, length(rv$dataIn)) - #browser() switch(rv.widgets$Normalization_method, @@ -547,7 +583,9 @@ PipelineProtein_Normalization_server <- function(id, ) }) - if(inherits(rv.custom$tmpAssay, "try-error")) { + + + if(inherits(rv.custom$tmpAssay, "try-error") || is.null(rv.custom$tmpAssay)) { MagellanNTK::mod_SweetAlert_server(id = 'sweetalert_perform_normalization', text = rv.custom$tmpAssay[[1]],