inst/shiny/ui.R

In aymanm/seuratOnline: User Interface to Seurat (Single Cell) in R Shiny

require(shinydashboard)
require(shinyjs)
require(shinyBS)
require(shinycssloaders)
require(DT)
require(shiny)
require(Seurat)
require(dplyr)
require(Matrix)

ui <- tagList(dashboardPage(
  dashboardHeader(title = "Seurat Online"),
  dashboardSidebar(
    sidebarMenu(id = "tabs",
      menuItem("Input Data", tabName = "datainput", icon = icon("upload")),
      menuItem("QC & Filter", tabName = "qcFilterTab", icon = icon("th")),
      menuItem("Vln Plot", tabName = "vlnplot", icon = icon("bar-chart")),
      menuItem("Filter & Normalize", tabName = "filterNormSelectTab", icon = icon("th")),
      menuItem("Dispersion Plot", tabName = "dispersionPlot", icon = icon("bar-chart")),
      menuItem("Scale and Run PCA", tabName = "runPcaTab", icon = icon("th")),
      menuItem("Viz PCA Plot", tabName = "vizPcaPlot", icon = icon("bar-chart")),
      menuItem("PCA Plot", tabName = "pcaPlot", icon = icon("bar-chart")),
      menuItem("PC Heatmap", tabName = "heatmapPlot", icon = icon("bar-chart")),
      menuItem("JackStraw", tabName = "jackStrawPlot", icon = icon("th")),
      menuItem("Cluster Cells", tabName = "clusterCells", icon = icon("th")),
      menuItem("TSNE (Non-linear)", tabName = "tsneTab", icon = icon("th")),
      menuItem("Download Seurat Obj", tabName = "finishTab", icon = icon("th")),
      menuItem("Cluster Markers", tabName = "findMarkersTab", icon = icon("th")),
      menuItem("Viz Markers", tabName = "vizMarkersTab", icon = icon("bar-chart"))
    )
  ),
  dashboardBody(
    shinyjs::useShinyjs(),
    extendShinyjs(script = "www/custom.js"),
    tags$head(
      tags$style(HTML(" .shiny-output-error-validation {color: darkred; } ")),
      tags$link(rel = "stylesheet", type = "text/css", href = "custom.css"),
      tags$link(rel = "stylesheet", type = "text/css", href = "buttons.css")
    ),
    tabItems(
             source("ui-tab-inputdata.R",local=TRUE)$value,
             source("ui-tab-qcfilter.R",local=TRUE)$value,
             source("ui-tab-vln.R",local = TRUE)$value,
             source("ui-tab-filterNormSelect.R",local = TRUE)$value,
             source("ui-tab-dispersionPlot.R",local = TRUE)$value,
             source("ui-tab-runPca.R",local = TRUE)$value,
             source("ui-tab-vizPcaPlot.R",local = TRUE)$value,
             source("ui-tab-pcaPlot.R",local = TRUE)$value,
             source("ui-tab-pcHeatmapPlot.R",local = TRUE)$value,
             source("ui-tab-jackStrawPlot.R",local = TRUE)$value,
             source("ui-tab-clusterCells.R",local = TRUE)$value,
             source("ui-tab-tsne.R",local = TRUE)$value,
             source("ui-tab-finish.R",local = TRUE)$value,
             source("ui-tab-findMarkers.R",local = TRUE)$value,
             source("ui-tab-vizMarkers.R",local = TRUE)$value
    )

  )

),
tags$footer(
  wellPanel(
  HTML('
       <p align="center" width="4">Developed and maintained by: Core Bioinformatics, Center for Genomics and Systems Biology, NYU Abu Dhabi</p>
       <p align="center" width="4">Using Seurat version 2.3.0</p>
       <p align="center" width="4"><strong>Acknowledgements: </strong></p>
        <p align="center" width="4">1) Rahul Satija, Andrew Butler and Paul Hoffman (2017). Seurat: Tools for Single Cell Genomics. R package
version 2.2.1. <a href="https://CRAN.R-project.org/package=Seurat" target="_blank">https://CRAN.R-project.org/package=Seurat</a></p>
       <p align="center" width="4">2) <a href="http://satijalab.org/seurat/" target="_blank">Satija Lab</a></p>')
  ))
)