In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

knitr::opts_chunk$set(echo = TRUE)

Design

Identify functions to be used and figures to be presented. Test with sample input. Try using plotly

ui.R

When using Modules import modulesUI

source(paste0(packagePath, "/modulesUI.R"), local = TRUE)

menuList

# list of menu Items
menuList <- list(
  shinydashboard::menuItem("Data Exploration",
                           # id="dataExplorationID",
                           tabName = "expore", icon = icon("wpexplorer"), startExpanded = FALSE,
                           shinydashboard::menuSubItem("Expression", tabName = "DE_expression"),
                           shinydashboard::menuSubItem("Panel plot", tabName = "DE_panelPlot")
                           # ,
                           # shinydashboard::menuSubItem("Panel plot factorials", tabName = "DE_panelPlotFact")
                           # shinydashboard::menuSubItem("Sorted plot", tabName = "DE_sortedPl")
  )
)

tabList

list of tab Items

tabList <- list( # DE_expression ---- expressionTab = shinydashboard::tabItem( "DE_expression", shinydashboardPlus::box( title = "Expression overview", solidHeader = TRUE, width = 12, status = "primary", fluidRow(div(tags$h3("Expression based on subset of cells"), align = "center")), tags$p("Similar to Co-expression - selection, but with a focus on subsets of cells and genes."), tags$p("Limit the cells to visualize by cluster or any other factorial."), tags$p("Visualize specific genes in 3D and over the current clustering (not changeable)."), tags$p("Projections will be not be effected by this sub selection."), br(), fluidRow( column( offset = 3, width = 12, cellSelectionUI("DE_Exp_dataInput") ) ), br(), fluidRow( column( width = 12, clusterUI("DE_expclusters")

using callr for killable processes

# variables/names : runScater, stopScater, maxMemory
# only lines with * are needed

# DE_scaterQC ----
  DE_scaterQCTab = shinydashboard::tabItem(
    "DE_scaterQC",
    shinydashboardPlus::box(
      title = "Quality control plot from the scater package", solidHeader = TRUE, 
      width = 12, status = "primary", height = "1627px",
      fluidRow(
        column(10, offset = 0,
*               actionButton("runScater", "apply changes", width = "40%"),
*               actionButton("stopScater", "stop calculations", width = "40%", class = "btn-danger")
        ),
        column(width = 2,
               sc_numericInput("maxMemory", "max memory to be used in GB",
                               min = 1, max = 2000, step = 1, value = 2))
      )
    )
  )

reactives.R

using callr for killable processes

outputs.R

list of available reactives

scEx

scEx_log

C3BI-pasteur-fr/UTechSCB-SCHNAPPs documentation built on Jan. 12, 2025, 1:16 p.m.