inst/shiny/ui.R

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

library(shiny)
library(shinyjs)
library(ComplexHeatmap)
library(limma)
library(ggplot2)
library(plotly)
library(data.table)
library(MAST)
library(colourpicker)
library(gridExtra)
library(cluster)
library(ggtree)
library(ape)
library(GSVA)
library(GSVAdata)
library(shinyalert)
library(enrichR)
library(matrixStats)
library(Biobase)
library(base)
library(SingleCellExperiment)
library(singleCellTK)
library(celda)
library(shinycssloaders)
library(shinythemes)
library(umap)
library(scater)
library(scran)
library(hypeR)
library(uwot)
library(reactable)

source("helpers.R")
source("colourGroupInput.R")
data("c2BroadSets")

#test internet connection for enrichR connectivity
internetConnection <- suppressWarnings(Biobase::testBioCConnection())

clusterChoice <- ""
sampleChoice <- ""
featureChoice <- ""
geneChoice <- ""
alertText <- ""
pcComponents <- ""
numClusters <- ""
currassays <- ""
currreddim <- ""
if (internetConnection){
  enrichedDB <- enrichR::listEnrichrDbs()$libraryName
} else {
  enrichedDB <- ""
}
numSamples <- 30
pcComponentsSelectedY <- NULL
if (!is.null(getShinyOption("inputSCEset"))){
  print(getShinyOption("inputSCEset"))
  numSamples <- ncol(getShinyOption("inputSCEset"))
  clusterChoice <- colnames(colData(getShinyOption("inputSCEset")))
  geneChoice <- rownames(getShinyOption("inputSCEset"))
  sampleChoice <- colnames(getShinyOption("inputSCEset"))
  featureChoice <- colnames(rowData(getShinyOption("inputSCEset")))
  pcComponents <- paste("PC", 1:numSamples, sep = "")
  pcComponentsSelectedY <- pcComponents[2]
  numClusters <- 1:numSamples
  currassays <- names(assays(getShinyOption("inputSCEset")))
  currreddim <- names(reducedDims(getShinyOption("inputSCEset")))
  alertText <- HTML("<div class='alert alert-success alert-dismissible'>\
                    <span class='glyphicon glyphicon-ok' aria-hidden='true'>\
                    </span> Successfully Uploaded from Command Line! <button \
                    type='button' class='close' data-dismiss='alert'>&times;\
                    </button></div>")
}

if (is.null(getShinyOption("theme"))){
  shinyTheme <- "flatly"
} else {
  shinyTheme <- getShinyOption("theme")
}

source("ui_01_upload.R", local = TRUE) #creates shinyPanelUpload variable
source("ui_02_filter.R", local = TRUE) #creates shinyPanelFilter variable
source("ui_03_1_genewise_vis.R", local = TRUE) #creates shinyPanelCluster variable
source("ui_03_2_samplewise_vis.R", local = TRUE) #creates shinyPanelCluster variable
source("ui_03_3_celda.R", local = TRUE) #creates shinyPanelCelda variable
source("ui_04_batchcorrect.R", local = TRUE) #creates shinyPanelBatchcorrect variable
source("ui_05_1_diffex.R", local = TRUE) #creates shinyPanelDiffex variable
source("ui_05_2_mast.R", local = TRUE) #creates shinyPanelMAST variable
source("ui_06_1_pathway.R", local = TRUE) #creates shinyPanelPathway variable
source("ui_06_2_enrichR.R", local = TRUE) #creates shinyPanelEnrichR variable
source("ui_06_3_hypeR.R", local = TRUE) #creates shinyPanelhypeR variable
source("ui_07_subsample.R", local = TRUE) #creates shinyPanelSubsample variable

if (is.null(getShinyOption("includeVersion"))){
  tooltitle <- paste("Single Cell Toolkit v",
                     packageVersion("singleCellTK"), sep = "")
} else {
  if (getShinyOption("includeVersion")){
    tooltitle <- paste("Single Cell Toolkit v",
                       packageVersion("singleCellTK"), sep = "")
  } else {
    tooltitle <- "Single Cell Toolkit"
  }
}

# Define UI for application that draws a histogram
shinyUI(
  navbarPage(
    tooltitle,
    theme = shinytheme(shinyTheme),
    #Upload Tab
    tabPanel("Upload", shinyPanelUpload),
    tabPanel("QC & Filtering", shinyPanelFilter),
    navbarMenu(
      "Visualization & Clustering",
      tabPanel("Genewise Visualization", shinyPanelVis),
      tabPanel("Cellwise Vis & Clustering", shinyPanelCluster),
      tabPanel("Celda", shinyPanelCelda)
    ),
    #tabPanel("Batch Correction", shinyPanelBatchcorrect),
    navbarMenu(
      "Differential Expression",
      tabPanel("Differential Expression", shinyPanelDiffex),
      tabPanel("MAST", shinyPanelMAST)
    ),
    navbarMenu(
      "Enrichment Analysis",
      tabPanel("hypeR", ShinyPanelHypeR),
      tabPanel("EnrichR", shinyPanelEnrichR),
      tabPanel("GSVA", shinyPanelPathway)
      
    ),
    tabPanel("Sample Size", shinyPanelSubsample),
    footer = includeHTML("www/footer.html")
  )
)