dev/PipelineCode/protein/test_mod_pipe_protein_Normalization.R

In samWieczorek/MSPipelines:

library(highcharter)
library(shinyjs)
library(DAPAR2)
library(DT)
library(tibble)
library(QFeatures)

source(file.path('../../../../R', 'config.R'), local=TRUE)$value
source(file.path('../../../../R', 'global.R'), local=TRUE)$value
source(file.path('../../../../R/PipelineCode/protein', 'mod_pipe_protein_Normalization.R'), local=TRUE)$value
source(file.path('../../../../R/Plots', 'mod_plots_tracking.R'), local=TRUE)$value
source(file.path('../../../../R', 'mod_navigation.R'), local=TRUE)$value
source(file.path('../../../../R', 'mod_settings.R'), local=TRUE)$value
source(file.path('../../../../R/Plots', 'mod_plots_density.R'), local=TRUE)$value
source(file.path('../../../../R/Plots', 'mod_plots_intensity.R'), local=TRUE)$value
source(file.path("../../../../R", "mod_popover_for_help.R"), local = TRUE)$value
source(file.path('../../../../R', 'mod_format_DT.R'), local=TRUE)$value
source(file.path('../../../../R', 'mod_infos_dataset.R'), local=TRUE)$value
source(file.path('../../../../R', 'mod_observe_dynamic_colourPicker_input.R'), local=TRUE)$value




options(shiny.fullstacktrace = FALSE)


ui <- fluidPage(
  tagList(
    mod_pipe_protein_Normalization_ui('pipe_norm'),
    mod_infos_dataset_ui('infos')
    # highchartOutput('test')
  )
)

# Define server logic to summarize and view selected dataset ----
server <- function(input, output, session) {
  
  utils::data(Exp1_R25_prot, package='DAPARdata2')
  
  rv <-reactiveValues(
    ret = NULL,
    current.obj = Exp1_R25_prot
  )
  
  
  # output$test <- renderHighchart({
  #   
  #   utils::data(Exp1_R25_pept, package='DAPARdata2')
  #   obj <- Exp1_R25_pept[1:1000,]
  #   conds <- colData(obj)[["Condition"]]
  #   obj <- normalizeD(obj, 2, name='norm', method='SumByColumns', conds=conds, type='overall')
  #   compareNormalizationD_HC(assay(obj, 2), assay(obj, 3), conds=conds, palette=NULL)
  # 
  # })
  # 
  
  rv$ret <- callModule(mod_pipe_protein_Normalization_server,
                       'pipe_norm',
                       obj = reactive({Exp1_R25_prot}),
                       ind = reactive({2}))
  
  callModule(mod_infos_dataset_server,'infos',
             obj = reactive({rv$current.obj}))
  
  
  observe({
    req(rv$ret())
    rv$current.obj <- rv$ret()
  })
}


shinyApp(ui, server)