inst/shiny/ui_01_import.R

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

exampleDatasets <- c() ## Need to add final small example data here
if ("TENxPBMCData" %in% rownames(installed.packages())){
  exampleDatasets <- c(exampleDatasets,
                       "PBMC 3K (10X)" = "pbmc3k",
                       "PBMC 4K (10X)" =  "pbmc4k",
                       "PBMC 6K (10X)" = "pbmc6k",
                       "PBMC 8K (10X)" = "pbmc8k",
                       "PBMC 33K (10X)" = "pbmc33k",
                       "PBMC 68K (10X)" = "pbmc68k")
}

if ("scRNAseq" %in% rownames(installed.packages())){
  exampleDatasets <- c(exampleDatasets,
                       "Fluidigm (Pollen et al, 2014)" = "fluidigm_pollen",
                       "Mouse Brain (Tasic et al, 2016)" = "allen_tasic")
}

shinyPanelImport <- fluidPage(
  useShinyjs(),
  tags$style(appCSS),
  tags$div(
    class = "jumbotron", style = "background-color:#ededed",
    tags$div(
      class = "container",
      h1("Single Cell Toolkit"),
      p("Filter, cluster, and analyze single cell RNA-Seq data"),
      p(
        "Need help?",
        tags$a(href = "https://www.sctk.science/index.html",
               "Read the docs.", target = "_blank")
      )
    )
  ),
  tags$br(),
  tags$div(
    class = "container",
    h1("Upload"),
    h5(tags$a(href = "https://www.sctk.science/articles/tab01_upload",
              "(help)", target = "_blank")),
    tags$hr(),
    hidden(wellPanel(id = "annotationData",
                     h3("Data summary"),
                     tableOutput("summarycontents"))),

    h3("Choose data source:"),
    radioButtons("uploadChoice", label = NULL, c("Import from a preprocessing tool" = 'directory',
                                                 "Upload files" = "files",
                                                 "Upload SingleCellExperiment or Seurat object stored in an RDS File" = "rds",
                                                 "Use example data" = "example")
    ),
    tags$hr(),
    conditionalPanel(condition = sprintf("input['%s'] == 'files'", "uploadChoice"),
                     h3("Upload data in tab separated text format:"),
                     fluidRow(
                       column(width = 4,
                              wellPanel(
                                h4("Example count file:"),
                                HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
                 <th>Cell1</th><th>Cell2</th><th>&#x2026;</th><th>CellN</th>
                 </tr></thead><tbody><tr class="odd"><td>Gene1</td><td>0</td>
                 <td>0</td><td>&#x2026;</td><td>0</td></tr><tr class="even">
                 <td>Gene2</td><td>5</td><td>6</td><td>&#x2026;</td><td>0</td>
                 </tr><tr class="odd"><td>Gene3</td><td>4</td><td>3</td>
                 <td>&#x2026;</td><td>8</td></tr><tr class="even">
                 <td>&#x2026;</td><td>&#x2026;</td><td>&#x2026;</td>
                 <td>&#x2026;</td><td>&#x2026;</td></tr><tr class="odd">
                 <td>GeneM</td><td>10</td><td>10</td><td>&#x2026;</td><td>10</td>
                 </tr></tbody></table>'),
            tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
                   "Download an example count file here.", target = "_blank"),
            tags$br(),
            tags$br(),
            fileInput(
              "countsfile",
              HTML(
                paste("Input assay (eg. counts, required):",
                tags$span(style = "color:red", "*", sep = ""))
              ),
              accept = c(
                "text/csv", "text/comma-separated-values", "mtx",
                "text/tab-separated-values", "text/plain", ".csv", ".tsv"
              )
            )
          ),
          h4("Input Assay Type:"),
          selectInput("inputAssayType", label = NULL,
                      c("counts", "normcounts", "logcounts", "cpm",
                        "logcpm", "tpm", "logtpm")
          )
        ),
        column(width = 4,
          wellPanel(
            h4("Example cell annotation file:"),
            HTML('<table class="table"><thead><tr class="header"><th>Cell</th>
                 <th>Annot1</th><th>&#x2026;</th></tr></thead><tbody><tr class="odd">
                 <td>Cell1</td><td>a</td><td>&#x2026;</td></tr><tr class="even">
                 <td>Cell2</td><td>a</td><td>&#x2026;</td></tr><tr class="odd">
                 <td>Cell3</td><td>b</td><td>&#x2026;</td></tr><tr class="even">
                 <td>&#x2026;</td><td>&#x2026;</td><td>&#x2026;</td></tr><tr class="odd"><td>CellN</td>
                 <td>b</td><td>&#x2026;</td></tr></tbody></table>'),
                                tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
                                       "Download an example annotation file here.", target = "_blank"),
                                tags$br(),
                                tags$br(),
                                fileInput(
                                  "annotFile", "Cell annotations (optional):",
                                  accept = c(
                                    "text/csv", "text/comma-separated-values",
                                    "text/tab-separated-values", "text/plain", ".csv", ".tsv"
                                  )
                                )
                              )
                       ),
                       column(width = 4,
                              wellPanel(
                                h4("Example feature file:"),
                                HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
               <th>Annot2</th><th>&#x2026;</th></tr></thead><tbody><tr class="odd">
                 <td>Gene1</td><td>a</td><td>&#x2026;</td></tr><tr class="even">
                 <td>Gene2</td><td>a</td><td>&#x2026;</td></tr><tr class="odd">
                 <td>Gene3</td><td>b</td><td>&#x2026;</td></tr><tr class="even">
                 <td>&#x2026;</td><td>&#x2026;</td><td>&#x2026;</td></tr><tr class="odd"><td>GeneM</td>
                 <td>b</td><td>&#x2026;</td></tr></tbody></table>'),
                                tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
                                       "Download an example feature file here.", target = "_blank"),
                                tags$br(),
                                tags$br(),
                                fileInput(
                                  "featureFile", "Feature annotations (optional):",
                                  accept = c(
                                    "text/csv", "text/comma-separated-values",
                                    "text/tab-separated-values", "text/plain", ".csv", ".tsv"
                                  )
                                )
                              )
                       )
                     ),
        actionButton("addFilesImport", "Add To Sample List")
    ),
    conditionalPanel(
      condition = sprintf("input['%s'] == 'example'", "uploadChoice"),
      h3("Choose Example Dataset:"),
      selectInput("selectExampleData", label = NULL, exampleDatasets),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'fluidigm_pollen'", "selectExampleData"),
        h3(tags$a(href = "http://dx.doi.org/10.1038/nbt.2967", "130 cells from (Pollen et al. 2014), 65 at high coverage and 65 at low coverage", target = "_blank")),
        "Transcriptomes of cell populations in both of low-coverage (~0.27 million reads per cell) and high-coverage (~5 million reads per cell) to identify cell-type-specific biomarkers, and to compare gene expression across samples specifically for cells of a given type as well as to reconstruct developmental lineages of related cell types. Data was loaded from the 'scRNASeq' package.",
        tags$br(),
        tags$br()
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'allen_tasic'", "selectExampleData"),
        h3(tags$a(href = "http://dx.doi.org/10.1038/nn.4216", "Mouse visual cortex cells from (Tasic et al. 2016)", target = "_blank")),
        "Subset of 379 cells from the mouse visual cortex. Data was loaded from the 'scRNASeq' package.",
        tags$br(),
        tags$br()
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'pbmc3k'", "selectExampleData"),
        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),
        "Data was loaded with the 'TENxPBMCData' package.",
        tags$br(),
        tags$br()
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'pbmc4k'", "selectExampleData"),
        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "4,430 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),
        "Data was loaded with the 'TENxPBMCData' package.",
        tags$br(),
        tags$br()
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'pbmc6k'", "selectExampleData"),
        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "5,419 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),
        "Data was loaded with the 'TENxPBMCData' package.",
        tags$br(),
        tags$br()
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'pbmc8k'", "selectExampleData"),
        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "8,381 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),
        "Data was loaded with the 'TENxPBMCData' package.",
        tags$br(),
        tags$br()
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'pbmc33k'", "selectExampleData"),
        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "33,148 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),
        "Data was loaded with the 'TENxPBMCData' package.",
        tags$br(),
        tags$br()
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'pbmc68k'", "selectExampleData"),
        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "68,579 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),
        "Data was loaded with the 'TENxPBMCData' package.",
        tags$br(),
        tags$br()
      ),
      actionButton("addExampleImport", "Add To Sample List")
    ),
    conditionalPanel(
      condition = sprintf("input['%s'] == 'rds'", "uploadChoice"),
      h3("Choose an RDS file that contains a SingleCellExperiment or Seurat object:"),
      fileInput(
        "rdsFile", "SingleCellExperiment RDS file:", accept = c(".rds", ".RDS")
      ),
      actionButton("addRDSImport", "Add To Sample List")
    ),
    conditionalPanel(
      condition = sprintf("input['%s'] == 'directory'", "uploadChoice"),
      tags$style(HTML("
      div {
        word-wrap: break-word;
      }
      ")),
      h3("Choose a Preprocessing Tool:"),
      radioButtons("algoChoice", label = NULL, c("Cell Ranger v2" = "cellRanger2",
                                                 "Cell Ranger v3" = "cellRanger3",
                                                 "STARsolo" = "starSolo",
                                                 "BUStools" = "busTools",
                                                 "SEQC" = "seqc",
                                                 "Optimus" = "optimus")
      ),
      tags$br(),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'cellRanger2'", "algoChoice"),
        actionButton("addCR2Sample", "Add a Sample"),
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'cellRanger3'", "algoChoice"),
        actionButton("addCR3Sample", "Add a Sample"),
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'starSolo'", "algoChoice"),
        wellPanel(
          h5("Please select the directory that contains your /Gene directory as your base directory. ")
        ),
        actionButton("addSSSample", "Add a Sample"),
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'busTools'", "algoChoice"),
        wellPanel(
          h5("Please select your /genecount directory as your base directory.")
        ),
        actionButton("addBUSSample", "Add a Sample"),
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'seqc'", "algoChoice"),
        wellPanel(
          h5("Please select the directory that contains your sample files as your base directory.")
        ),
        actionButton("addSEQSample", "Add a Sample"),
      ),
      conditionalPanel(
        condition = sprintf("input['%s'] == 'optimus'", "algoChoice"),
        wellPanel(
          h5("Please select the directory that contains the following four directories - call-MergeCountFiles, call-MergeCellMetrics, call-MergeGeneMetrics, call-RunEmptyDrops - as your base directory.")
        ),
        actionButton("addOptSample", "Add a Sample"),
      ),
    ),
    tags$hr(),
    wellPanel(
      h4("Samples to Import:"),
      fluidRow(
        column(3, tags$b("Type")),
        column(3, tags$b("Location")),
        column(3, tags$b("Sample Name")),
        column(3, tags$b("Remove"))
      ),
      tags$div(id = "newSampleImport"),
      tags$br(),
      tags$br(),
      actionButton("clearAllImport", "Clear Samples")
    ),
    radioButtons("combineSCEChoice", label = NULL, c("Add to existing SCE object" = 'addToExistingSCE',
                                                 "Overwrite existing SCE object" = "overwriteSCE")
    ),
    withBusyIndicatorUI(
      actionButton("uploadData", "Import")
    ),

    tags$div(
      class = "container",
      p("")
    )
  )
  #includeHTML("www/footer.html")
)