| ... | ... |
@@ -22,17 +22,22 @@ nonLinearWorkflow <- function(input, output, session, parent, |
| 22 | 22 |
ns <- session$ns |
| 23 | 23 |
|
| 24 | 24 |
output$ui <- renderUI({
|
| 25 |
- bsCollapsePanel(tagList(icon("chevron-circle-down"), "Downstream Analysis"),
|
|
| 26 |
- uiOutput(ns("de")),
|
|
| 27 |
- uiOutput(ns("pa")),
|
|
| 28 |
- uiOutput(ns("qcf")),
|
|
| 29 |
- uiOutput(ns("nbc")),
|
|
| 30 |
- uiOutput(ns("cw")),
|
|
| 31 |
- uiOutput(ns("dr")),
|
|
| 32 |
- uiOutput(ns("fs")),
|
|
| 33 |
- uiOutput(ns("cl")),
|
|
| 34 |
- uiOutput(ns("cv")),
|
|
| 35 |
- style = "success") |
|
| 25 |
+ bsCollapse( |
|
| 26 |
+ open = "Next Steps", |
|
| 27 |
+ bsCollapsePanel("Next Steps",
|
|
| 28 |
+ uiOutput(ns("de")),
|
|
| 29 |
+ uiOutput(ns("pa")),
|
|
| 30 |
+ uiOutput(ns("qcf")),
|
|
| 31 |
+ uiOutput(ns("nbc")),
|
|
| 32 |
+ uiOutput(ns("cw")),
|
|
| 33 |
+ uiOutput(ns("dr")),
|
|
| 34 |
+ uiOutput(ns("fs")),
|
|
| 35 |
+ uiOutput(ns("cl")),
|
|
| 36 |
+ uiOutput(ns("cv")),
|
|
| 37 |
+ style = "success" |
|
| 38 |
+ ) |
|
| 39 |
+ ) |
|
| 40 |
+ |
|
| 36 | 41 |
}) |
| 37 | 42 |
|
| 38 | 43 |
if(de){
|
| ... | ... |
@@ -145,11 +145,32 @@ shinyServer(function(input, output, session) {
|
| 145 | 145 |
} |
| 146 | 146 |
|
| 147 | 147 |
updateFeatureAnnots <- function(){
|
| 148 |
+ |
|
| 148 | 149 |
selectRowData <- colnames(rowData(vals$counts)) |
| 150 |
+ my_list <- data.frame() |
|
| 151 |
+ for(i in selectRowData) {
|
|
| 152 |
+ my_list[i,1] <- paste0(i, " (e.g. ", paste(head(rowData(vals$counts)[,i], n = 3), collapse = ","), ")") |
|
| 153 |
+ } |
|
| 154 |
+ selectRowDataWithExamples <- as.character(my_list[,1]) |
|
| 155 |
+ |
|
| 156 |
+ |
|
| 157 |
+ selectNonNARowData <- names(apply(rowData(vals$counts), 2, anyNA)[apply(rowData(vals$counts), 2, anyNA) == FALSE]) |
|
| 158 |
+ my_list2 <- data.frame() |
|
| 159 |
+ for(j in selectNonNARowData) {
|
|
| 160 |
+ my_list2[j,1] <- paste0(j, " (e.g. ", paste(head(rowData(vals$counts)[,j], n = 3), collapse = ","), ")") |
|
| 161 |
+ } |
|
| 162 |
+ selectNonNARowDataWithExamples <- as.character(my_list2[,1]) |
|
| 163 |
+ |
|
| 164 |
+ Default <- paste0("Default (e.g. ", paste(head(rownames(vals$counts), n = 3), collapse = ","), ")")
|
|
| 165 |
+ |
|
| 149 | 166 |
updateSelectInput(session, "gsByParam", |
| 150 | 167 |
choices = c("rownames", selectRowData))
|
| 151 | 168 |
updateSelectInput(session, "importFeatureDispOpt", |
| 152 |
- choices = c("Rownames (Default)", selectRowData))
|
|
| 169 |
+ choices = c(Default, |
|
| 170 |
+ selectRowDataWithExamples)) |
|
| 171 |
+ updateSelectInput(session, "importFeatureNamesOpt", |
|
| 172 |
+ choices = c(Default, |
|
| 173 |
+ selectNonNARowDataWithExamples)) |
|
| 153 | 174 |
updateSelectInput(session, "filteredFeature", |
| 154 | 175 |
choices = c("none", selectRowData))
|
| 155 | 176 |
updateSelectInput(session, "hvgPlotFeatureDisplay", |
| ... | ... |
@@ -435,7 +456,7 @@ shinyServer(function(input, output, session) {
|
| 435 | 456 |
count <- 0 |
| 436 | 457 |
if (!is.na(path)) {
|
| 437 | 458 |
# Add Reference selection for cellRangerV2 |
| 438 |
- if (input$algoChoice == "cellRanger2") {
|
|
| 459 |
+ if (input$uploadChoice == "cellRanger2") {
|
|
| 439 | 460 |
## Identify available reference |
| 440 | 461 |
firstSampleDir <- list.dirs(path, recursive = FALSE)[1] |
| 441 | 462 |
refPath <- file.path(firstSampleDir, "outs/filtered_gene_bc_matrices") |
| ... | ... |
@@ -492,7 +513,7 @@ shinyServer(function(input, output, session) {
|
| 492 | 513 |
collapse = .Platform$file.sep)) |
| 493 | 514 |
path <- dirPaths$sDirectory |
| 494 | 515 |
if (!is.na(path)) {
|
| 495 |
- if (input$algoChoice == "cellRanger2") {
|
|
| 516 |
+ if (input$uploadChoice == "cellRanger2") {
|
|
| 496 | 517 |
## Identify available reference |
| 497 | 518 |
refPath <- file.path(path, "outs/filtered_gene_bc_matrices") |
| 498 | 519 |
refList <- basename(list.dirs(refPath, recursive = FALSE)) |
| ... | ... |
@@ -582,7 +603,7 @@ shinyServer(function(input, output, session) {
|
| 582 | 603 |
} else {
|
| 583 | 604 |
allDirs <- list.dirs(basePath, recursive = FALSE) |
| 584 | 605 |
# if we are adding a new CellRangerV2 sample |
| 585 |
- if (input$algoChoice == "cellRanger2") {
|
|
| 606 |
+ if (input$uploadChoice == "cellRanger2") {
|
|
| 586 | 607 |
allUI <- vector() |
| 587 | 608 |
allIDs <- vector() |
| 588 | 609 |
count <- 0 |
| ... | ... |
@@ -671,6 +692,7 @@ shinyServer(function(input, output, session) {
|
| 671 | 692 |
) |
| 672 | 693 |
removeModal() |
| 673 | 694 |
} |
| 695 |
+ updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))
|
|
| 674 | 696 |
}) |
| 675 | 697 |
|
| 676 | 698 |
# event listeners for Cell Ranger import modals' OK buttons |
| ... | ... |
@@ -682,7 +704,7 @@ shinyServer(function(input, output, session) {
|
| 682 | 704 |
showModal(importCRSDir(failed = TRUE)) |
| 683 | 705 |
} else {
|
| 684 | 706 |
# add the files to the appropriate reactiveValues |
| 685 |
- if (input$algoChoice == "cellRanger2") {
|
|
| 707 |
+ if (input$uploadChoice == "cellRanger2") {
|
|
| 686 | 708 |
id <- paste0("snewSampleCR2", allImportEntries$id_count)
|
| 687 | 709 |
entry <- list(type="cellRanger2", id=id, |
| 688 | 710 |
params=list(cellRangerDirs = dirname(samplePath), |
| ... | ... |
@@ -698,7 +720,7 @@ shinyServer(function(input, output, session) {
|
| 698 | 720 |
allImportEntries$id_count <- allImportEntries$id_count + 1 |
| 699 | 721 |
} |
| 700 | 722 |
# add new row to table |
| 701 |
- addToGeneralSampleTable(input$algoChoice, id, samplePath, input$sSampleID) |
|
| 723 |
+ addToGeneralSampleTable(input$uploadChoice, id, samplePath, input$sSampleID) |
|
| 702 | 724 |
# handler to remove the sample that was just added |
| 703 | 725 |
observeEvent(input[[paste0("remove", id)]],{
|
| 704 | 726 |
removeUI( |
| ... | ... |
@@ -716,6 +738,8 @@ shinyServer(function(input, output, session) {
|
| 716 | 738 |
}) |
| 717 | 739 |
removeModal() |
| 718 | 740 |
} |
| 741 |
+ updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))
|
|
| 742 |
+ |
|
| 719 | 743 |
}) |
| 720 | 744 |
|
| 721 | 745 |
# data directory |
| ... | ... |
@@ -724,7 +748,7 @@ shinyServer(function(input, output, session) {
|
| 724 | 748 |
if ((!nzchar(input$dSampleID)) || (identical(dataPath, character(0)))) {
|
| 725 | 749 |
showModal(importCRDDir(failed = TRUE)) |
| 726 | 750 |
} else {
|
| 727 |
- if (input$algoChoice == "cellRanger2") {
|
|
| 751 |
+ if (input$uploadChoice == "cellRanger2") {
|
|
| 728 | 752 |
id <- paste0("dnewSampleCR2", allImportEntries$id_count)
|
| 729 | 753 |
entry <- list(type="cellRanger2", id=id, |
| 730 | 754 |
params=list(dataDir = dataPath, |
| ... | ... |
@@ -738,7 +762,7 @@ shinyServer(function(input, output, session) {
|
| 738 | 762 |
allImportEntries$id_count <- allImportEntries$id_count + 1 |
| 739 | 763 |
} |
| 740 | 764 |
# add new row to table |
| 741 |
- addToGeneralSampleTable(input$algoChoice, id, dataPath, input$dSampleID) |
|
| 765 |
+ addToGeneralSampleTable(input$uploadChoice, id, dataPath, input$dSampleID) |
|
| 742 | 766 |
observeEvent(input[[paste0("remove", id)]],{
|
| 743 | 767 |
removeUI( |
| 744 | 768 |
selector = paste0("#", id)
|
| ... | ... |
@@ -755,6 +779,8 @@ shinyServer(function(input, output, session) {
|
| 755 | 779 |
}) |
| 756 | 780 |
removeModal() |
| 757 | 781 |
} |
| 782 |
+ updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))
|
|
| 783 |
+ |
|
| 758 | 784 |
}) |
| 759 | 785 |
|
| 760 | 786 |
# event handler for pressing OK on the import modal |
| ... | ... |
@@ -765,29 +791,29 @@ shinyServer(function(input, output, session) {
|
| 765 | 791 |
showModal(importModal(failed = TRUE)) |
| 766 | 792 |
} else {
|
| 767 | 793 |
entry <- list() |
| 768 |
- if (input$algoChoice == "starSolo") {
|
|
| 794 |
+ if (input$uploadChoice == "starSolo") {
|
|
| 769 | 795 |
id <- paste0("newSampleSS", allImportEntries$id_count)
|
| 770 | 796 |
entry <- list(type="starSolo", id = id, params=list(STARsoloDirs = basePath, samples = input$sampleName)) |
| 771 | 797 |
allImportEntries$samples <- c(allImportEntries$samples, list(entry)) |
| 772 | 798 |
allImportEntries$id_count <- allImportEntries$id_count+1 |
| 773 |
- } else if (input$algoChoice == "busTools") {
|
|
| 799 |
+ } else if (input$uploadChoice == "busTools") {
|
|
| 774 | 800 |
id <- paste0("newSampleBUS", allImportEntries$id_count)
|
| 775 | 801 |
entry <- list(type="busTools", id = id, params=list(BUStoolsDirs = basePath, samples = input$sampleName)) |
| 776 | 802 |
allImportEntries$samples <- c(allImportEntries$samples, list(entry)) |
| 777 | 803 |
allImportEntries$id_count <- allImportEntries$id_count+1 |
| 778 |
- } else if (input$algoChoice == "seqc") {
|
|
| 804 |
+ } else if (input$uploadChoice == "seqc") {
|
|
| 779 | 805 |
id <- paste0("newSampleSEQ", allImportEntries$id_count)
|
| 780 | 806 |
entry <- list(type="seqc", id = id, params=list(seqcDirs = basePath, prefix = input$sampleID, samples = input$sampleName)) |
| 781 | 807 |
updateTextInput(session, "sampleID", value = "") |
| 782 | 808 |
allImportEntries$samples <- c(allImportEntries$samples, list(entry)) |
| 783 | 809 |
allImportEntries$id_count <- allImportEntries$id_count+1 |
| 784 |
- } else if (input$algoChoice == "optimus") {
|
|
| 810 |
+ } else if (input$uploadChoice == "optimus") {
|
|
| 785 | 811 |
id <- paste0("newSampleOpt", allImportEntries$id_count)
|
| 786 | 812 |
entry <- list(type="optimus", id = id, params=list(OptimusDirs = basePath, samples = input$sampleName)) |
| 787 | 813 |
allImportEntries$samples <- c(allImportEntries$samples, list(entry)) |
| 788 | 814 |
allImportEntries$id_count <- allImportEntries$id_count+1 |
| 789 | 815 |
} |
| 790 |
- addToGeneralSampleTable(input$algoChoice, id, basePath, input$sampleName) |
|
| 816 |
+ addToGeneralSampleTable(input$uploadChoice, id, basePath, input$sampleName) |
|
| 791 | 817 |
observeEvent(input[[paste0("remove", id)]],{
|
| 792 | 818 |
removeUI( |
| 793 | 819 |
selector = paste0("#", id)
|
| ... | ... |
@@ -804,6 +830,8 @@ shinyServer(function(input, output, session) {
|
| 804 | 830 |
}) |
| 805 | 831 |
removeModal() |
| 806 | 832 |
} |
| 833 |
+ updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))
|
|
| 834 |
+ |
|
| 807 | 835 |
}) |
| 808 | 836 |
|
| 809 | 837 |
# Event handler to import a file input |
| ... | ... |
@@ -844,6 +872,8 @@ shinyServer(function(input, output, session) {
|
| 844 | 872 |
} |
| 845 | 873 |
allImportEntries$samples <- allImportEntries$samples[toRemove] |
| 846 | 874 |
}) |
| 875 |
+ updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))
|
|
| 876 |
+ |
|
| 847 | 877 |
}) |
| 848 | 878 |
|
| 849 | 879 |
# Event handler to import an example input |
| ... | ... |
@@ -879,6 +909,8 @@ shinyServer(function(input, output, session) {
|
| 879 | 909 |
} |
| 880 | 910 |
allImportEntries$samples <- allImportEntries$samples[toRemove] |
| 881 | 911 |
}) |
| 912 |
+ updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))
|
|
| 913 |
+ |
|
| 882 | 914 |
}) |
| 883 | 915 |
|
| 884 | 916 |
# Event handler to import an RDS input |
| ... | ... |
@@ -904,6 +936,8 @@ shinyServer(function(input, output, session) {
|
| 904 | 936 |
} |
| 905 | 937 |
allImportEntries$samples <- allImportEntries$samples[toRemove] |
| 906 | 938 |
}) |
| 939 |
+ updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))
|
|
| 940 |
+ |
|
| 907 | 941 |
}) |
| 908 | 942 |
|
| 909 | 943 |
# Event handler for "Upload" button on import page |
| ... | ... |
@@ -1006,6 +1040,8 @@ shinyServer(function(input, output, session) {
|
| 1006 | 1040 |
# datasets. Otherwise, errors may pop out when Shiny listens to the new |
| 1007 | 1041 |
# object but cannot find the old result. |
| 1008 | 1042 |
}) |
| 1043 |
+ updateCollapse(session = session, "importUI", style = list("2. Create dataset:" = "success"))
|
|
| 1044 |
+ |
|
| 1009 | 1045 |
callModule(module = nonLinearWorkflow, id = "nlw-import", parent = session, qcf = TRUE) |
| 1010 | 1046 |
|
| 1011 | 1047 |
.loadClose() # close the notification spinner and console log |
| ... | ... |
@@ -1332,13 +1368,20 @@ shinyServer(function(input, output, session) {
|
| 1332 | 1368 |
if (!is.null(vals$counts)) {
|
| 1333 | 1369 |
withBusyIndicatorServer("importFeatureDipSet", {
|
| 1334 | 1370 |
selected <- NULL |
| 1335 |
- if (!input$importFeatureDispOpt == "Rownames (Default)") {
|
|
| 1336 |
- selected <- input$importFeatureDispOpt |
|
| 1371 |
+ |
|
| 1372 |
+ if (!stringr::word(input$importFeatureDispOpt, 1) == "Default") {
|
|
| 1373 |
+ featureName <- word(input$importFeatureDispOpt, 1) |
|
| 1374 |
+ selected <- featureName |
|
| 1375 |
+ } |
|
| 1376 |
+ if (!stringr::word(input$importFeatureNamesOpt, 1) == "Default") {
|
|
| 1377 |
+ featureID <- word(input$importFeatureNamesOpt, 1) |
|
| 1378 |
+ rownames(vals$counts) <- rowData(vals$counts)[[featureID]] |
|
| 1337 | 1379 |
} |
| 1338 | 1380 |
vals$counts <- setSCTKDisplayRow(vals$counts, selected) |
| 1339 | 1381 |
updateFeatureDisplaySelect(selected = selected) |
| 1340 | 1382 |
}) |
| 1341 | 1383 |
} |
| 1384 |
+ updateCollapse(session = session, "importUI", style = list("3. Data summary:" = "success"))
|
|
| 1342 | 1385 |
}) |
| 1343 | 1386 |
updateFeatureDisplaySelect <- function(selected = NULL, updateOptions = FALSE) |
| 1344 | 1387 |
{
|
| ... | ... |
@@ -2125,7 +2168,7 @@ shinyServer(function(input, output, session) {
|
| 2125 | 2168 |
}, striped = TRUE, border = TRUE, align = "c", spacing = "l") |
| 2126 | 2169 |
|
| 2127 | 2170 |
#Render summary table |
| 2128 |
- output$summarycontents <- renderTable({
|
|
| 2171 |
+ output$summarycontents <- DT::renderDataTable({
|
|
| 2129 | 2172 |
req(vals$counts) |
| 2130 | 2173 |
if ("Sample" %in% names(colData(vals$counts))) {
|
| 2131 | 2174 |
sampleVar <- "Sample" |
| ... | ... |
@@ -2138,7 +2181,7 @@ shinyServer(function(input, output, session) {
|
| 2138 | 2181 |
singleCellTK::summarizeSCE(inSCE = vals$counts, |
| 2139 | 2182 |
useAssay = NULL, |
| 2140 | 2183 |
sampleVariableName = sampleVar) |
| 2141 |
- }, striped = TRUE, border = TRUE, align = "c", spacing = "l") |
|
| 2184 |
+ }) |
|
| 2142 | 2185 |
|
| 2143 | 2186 |
|
| 2144 | 2187 |
#Reset the data to the original uploaded dataset |
| ... | ... |
@@ -16,6 +16,7 @@ if ("scRNAseq" %in% rownames(installed.packages())){
|
| 16 | 16 |
"NestorowaHSC (Nestorowa et al, 2016)" = "NestorowaHSCData") |
| 17 | 17 |
} |
| 18 | 18 |
|
| 19 |
+# User Interface for import Workflow --- |
|
| 19 | 20 |
shinyPanelImport <- fluidPage( |
| 20 | 21 |
useShinyjs(), |
| 21 | 22 |
tags$style(appCSS), |
| ... | ... |
@@ -33,26 +34,36 @@ shinyPanelImport <- fluidPage( |
| 33 | 34 |
) |
| 34 | 35 |
), |
| 35 | 36 |
tags$br(), |
| 36 |
- tags$div( |
|
| 37 |
- class = "container", |
|
| 38 |
- h1("Import"),
|
|
| 39 |
- h5(tags$a(href = paste0(docs.artPath, "import_data.html"), |
|
| 40 |
- "(help)", target = "_blank")), |
|
| 41 |
- tags$hr(), |
|
| 42 |
- h3("1. Choose data source:"),
|
|
| 43 |
- radioButtons("uploadChoice", label = NULL, c("Import from a preprocessing tool" = 'directory',
|
|
| 44 |
- "Import from flat files (.csv, .txt, .mtx)" = "files", |
|
| 45 |
- "Upload SingleCellExperiment or Seurat object stored in an RDS File" = "rds", |
|
| 46 |
- "Import example datasets" = "example") |
|
| 47 |
- ), |
|
| 48 |
- tags$hr(), |
|
| 49 |
- conditionalPanel(condition = sprintf("input['%s'] == 'files'", "uploadChoice"),
|
|
| 50 |
- h3("2. Upload data in tab separated text format:"),
|
|
| 51 |
- fluidRow( |
|
| 52 |
- column(width = 4, |
|
| 53 |
- wellPanel( |
|
| 54 |
- h4("Example count file:"),
|
|
| 55 |
- HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
|
|
| 37 |
+ |
|
| 38 |
+ h1("Import"),
|
|
| 39 |
+ h5(tags$a(href = paste0(docs.artPath, "import_data.html"), |
|
| 40 |
+ "(help)", target = "_blank")), |
|
| 41 |
+ tags$hr(), |
|
| 42 |
+ |
|
| 43 |
+ bsCollapse( |
|
| 44 |
+ id = "importUI", |
|
| 45 |
+ open = "1. Add sample to import:", |
|
| 46 |
+ bsCollapsePanel( |
|
| 47 |
+ "1. Add sample to import:", |
|
| 48 |
+ radioButtons("uploadChoice", label = NULL, c("Cell Ranger (Version 3 or above)" = "cellRanger3",
|
|
| 49 |
+ "Cell Ranger (Version 2)" = "cellRanger2", |
|
| 50 |
+ "STARsolo" = "starSolo", |
|
| 51 |
+ "BUStools" = "busTools", |
|
| 52 |
+ "SEQC" = "seqc", |
|
| 53 |
+ "Optimus" = "optimus", |
|
| 54 |
+ #"Import from a preprocessing tool" = 'directory', |
|
| 55 |
+ "Import from flat files (.csv, .txt, .mtx)" = "files", |
|
| 56 |
+ "Upload SingleCellExperiment or Seurat object stored in an RDS File" = "rds", |
|
| 57 |
+ "Import example datasets" = "example") |
|
| 58 |
+ ), |
|
| 59 |
+ tags$hr(), |
|
| 60 |
+ conditionalPanel(condition = sprintf("input['%s'] == 'files'", "uploadChoice"),
|
|
| 61 |
+ h3("Upload data in tab separated text format:"),
|
|
| 62 |
+ fluidRow( |
|
| 63 |
+ column(width = 4, |
|
| 64 |
+ wellPanel( |
|
| 65 |
+ h4("Example count file:"),
|
|
| 66 |
+ HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
|
|
| 56 | 67 |
<th>Cell1</th><th>Cell2</th><th>…</th><th>CellN</th> |
| 57 | 68 |
</tr></thead><tbody><tr class="odd"><td>Gene1</td><td>0</td> |
| 58 | 69 |
<td>0</td><td>…</td><td>0</td></tr><tr class="even"> |
| ... | ... |
@@ -63,257 +74,264 @@ shinyPanelImport <- fluidPage( |
| 63 | 74 |
<td>…</td><td>…</td></tr><tr class="odd"> |
| 64 | 75 |
<td>GeneM</td><td>10</td><td>10</td><td>…</td><td>10</td> |
| 65 | 76 |
</tr></tbody></table>'), |
| 66 |
- tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8", |
|
| 67 |
- "Download an example count file here.", target = "_blank"), |
|
| 68 |
- tags$br(), |
|
| 69 |
- tags$br(), |
|
| 70 |
- fileInput( |
|
| 71 |
- "countsfile", |
|
| 72 |
- HTML( |
|
| 73 |
- paste("Input assay (eg. counts, required):",
|
|
| 74 |
- tags$span(style = "color:red", "*", sep = "")) |
|
| 75 |
- ), |
|
| 76 |
- accept = c( |
|
| 77 |
- "text/csv", "text/comma-separated-values", "mtx", |
|
| 78 |
- "text/tab-separated-values", "text/plain", ".csv", ".tsv" |
|
| 79 |
- ) |
|
| 80 |
- ) |
|
| 81 |
- ), |
|
| 82 |
- h4("Input Assay Type:"),
|
|
| 83 |
- selectInput("inputAssayType", label = NULL,
|
|
| 84 |
- c("counts", "normcounts", "logcounts", "cpm",
|
|
| 85 |
- "logcpm", "tpm", "logtpm") |
|
| 86 |
- ) |
|
| 87 |
- ), |
|
| 88 |
- column(width = 4, |
|
| 89 |
- wellPanel( |
|
| 90 |
- h4("Example cell annotation file:"),
|
|
| 91 |
- HTML('<table class="table"><thead><tr class="header"><th>Cell</th>
|
|
| 77 |
+ tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8", |
|
| 78 |
+ "Download an example count file here.", target = "_blank"), |
|
| 79 |
+ tags$br(), |
|
| 80 |
+ tags$br(), |
|
| 81 |
+ fileInput( |
|
| 82 |
+ "countsfile", |
|
| 83 |
+ HTML( |
|
| 84 |
+ paste("Input assay (eg. counts, required):",
|
|
| 85 |
+ tags$span(style = "color:red", "*", sep = "")) |
|
| 86 |
+ ), |
|
| 87 |
+ accept = c( |
|
| 88 |
+ "text/csv", "text/comma-separated-values", "mtx", |
|
| 89 |
+ "text/tab-separated-values", "text/plain", ".csv", ".tsv" |
|
| 90 |
+ ) |
|
| 91 |
+ ) |
|
| 92 |
+ ), |
|
| 93 |
+ h4("Input Assay Type:"),
|
|
| 94 |
+ selectInput("inputAssayType", label = NULL,
|
|
| 95 |
+ c("counts", "normcounts", "logcounts", "cpm",
|
|
| 96 |
+ "logcpm", "tpm", "logtpm") |
|
| 97 |
+ ) |
|
| 98 |
+ ), |
|
| 99 |
+ column(width = 4, |
|
| 100 |
+ wellPanel( |
|
| 101 |
+ h4("Example cell annotation file:"),
|
|
| 102 |
+ HTML('<table class="table"><thead><tr class="header"><th>Cell</th>
|
|
| 92 | 103 |
<th>Annot1</th><th>…</th></tr></thead><tbody><tr class="odd"> |
| 93 | 104 |
<td>Cell1</td><td>a</td><td>…</td></tr><tr class="even"> |
| 94 | 105 |
<td>Cell2</td><td>a</td><td>…</td></tr><tr class="odd"> |
| 95 | 106 |
<td>Cell3</td><td>b</td><td>…</td></tr><tr class="even"> |
| 96 | 107 |
<td>…</td><td>…</td><td>…</td></tr><tr class="odd"><td>CellN</td> |
| 97 | 108 |
<td>b</td><td>…</td></tr></tbody></table>'), |
| 98 |
- tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J", |
|
| 99 |
- "Download an example annotation file here.", target = "_blank"), |
|
| 100 |
- tags$br(), |
|
| 101 |
- tags$br(), |
|
| 102 |
- fileInput( |
|
| 103 |
- "annotFile", "Cell annotations (optional):", |
|
| 104 |
- accept = c( |
|
| 105 |
- "text/csv", "text/comma-separated-values", |
|
| 106 |
- "text/tab-separated-values", "text/plain", ".csv", ".tsv" |
|
| 109 |
+ tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J", |
|
| 110 |
+ "Download an example annotation file here.", target = "_blank"), |
|
| 111 |
+ tags$br(), |
|
| 112 |
+ tags$br(), |
|
| 113 |
+ fileInput( |
|
| 114 |
+ "annotFile", "Cell annotations (optional):", |
|
| 115 |
+ accept = c( |
|
| 116 |
+ "text/csv", "text/comma-separated-values", |
|
| 117 |
+ "text/tab-separated-values", "text/plain", ".csv", ".tsv" |
|
| 118 |
+ ) |
|
| 107 | 119 |
) |
| 108 | 120 |
) |
| 109 |
- ) |
|
| 110 |
- ), |
|
| 111 |
- column(width = 4, |
|
| 112 |
- wellPanel( |
|
| 113 |
- h4("Example feature file:"),
|
|
| 114 |
- HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
|
|
| 121 |
+ ), |
|
| 122 |
+ column(width = 4, |
|
| 123 |
+ wellPanel( |
|
| 124 |
+ h4("Example feature file:"),
|
|
| 125 |
+ HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
|
|
| 115 | 126 |
<th>Annot2</th><th>…</th></tr></thead><tbody><tr class="odd"> |
| 116 | 127 |
<td>Gene1</td><td>a</td><td>…</td></tr><tr class="even"> |
| 117 | 128 |
<td>Gene2</td><td>a</td><td>…</td></tr><tr class="odd"> |
| 118 | 129 |
<td>Gene3</td><td>b</td><td>…</td></tr><tr class="even"> |
| 119 | 130 |
<td>…</td><td>…</td><td>…</td></tr><tr class="odd"><td>GeneM</td> |
| 120 | 131 |
<td>b</td><td>…</td></tr></tbody></table>'), |
| 121 |
- tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O", |
|
| 122 |
- "Download an example feature file here.", target = "_blank"), |
|
| 123 |
- tags$br(), |
|
| 124 |
- tags$br(), |
|
| 125 |
- fileInput( |
|
| 126 |
- "featureFile", "Feature annotations (optional):", |
|
| 127 |
- accept = c( |
|
| 128 |
- "text/csv", "text/comma-separated-values", |
|
| 129 |
- "text/tab-separated-values", "text/plain", ".csv", ".tsv" |
|
| 132 |
+ tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O", |
|
| 133 |
+ "Download an example feature file here.", target = "_blank"), |
|
| 134 |
+ tags$br(), |
|
| 135 |
+ tags$br(), |
|
| 136 |
+ fileInput( |
|
| 137 |
+ "featureFile", "Feature annotations (optional):", |
|
| 138 |
+ accept = c( |
|
| 139 |
+ "text/csv", "text/comma-separated-values", |
|
| 140 |
+ "text/tab-separated-values", "text/plain", ".csv", ".tsv" |
|
| 141 |
+ ) |
|
| 130 | 142 |
) |
| 131 | 143 |
) |
| 132 |
- ) |
|
| 133 |
- ) |
|
| 134 |
- ), |
|
| 135 |
- actionButton("addFilesImport", "Add To Sample List")
|
|
| 136 |
- ), |
|
| 137 |
- conditionalPanel( |
|
| 138 |
- condition = sprintf("input['%s'] == 'example'", "uploadChoice"),
|
|
| 139 |
- h3("2. Choose Example Dataset:"),
|
|
| 140 |
- selectInput("selectExampleData", label = NULL, exampleDatasets),
|
|
| 141 |
- conditionalPanel( |
|
| 142 |
- condition = sprintf("input['%s'] == 'fluidigm_pollen'", "selectExampleData"),
|
|
| 143 |
- h3(tags$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")), |
|
| 144 |
- "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.", |
|
| 145 |
- tags$br(), |
|
| 146 |
- tags$br() |
|
| 147 |
- ), |
|
| 148 |
- conditionalPanel( |
|
| 149 |
- condition = sprintf("input['%s'] == 'allen_tasic'", "selectExampleData"),
|
|
| 150 |
- h3(tags$a(href = "http://dx.doi.org/10.1038/nn.4216", "Mouse visual cortex cells from (Tasic et al. 2016)", target = "_blank")), |
|
| 151 |
- "Subset of 379 cells from the mouse visual cortex. Data was loaded from the 'scRNASeq' package.", |
|
| 152 |
- tags$br(), |
|
| 153 |
- tags$br() |
|
| 154 |
- ), |
|
| 155 |
- conditionalPanel( |
|
| 156 |
- condition = sprintf("input['%s'] == 'NestorowaHSCData'", "selectExampleData"),
|
|
| 157 |
- h3(tags$a(href = "https://www.nature.com/articles/nbt.2967", "1920 Mouse haematopoietic stem cells from (Nestorowa et al. 2015).", target= "_blank")), |
|
| 158 |
- "Data was loaded from the 'scRNASeq' package.", |
|
| 159 |
- tags$br(), |
|
| 160 |
- tags$br() |
|
| 161 |
- ), |
|
| 162 |
- conditionalPanel( |
|
| 163 |
- condition = sprintf("input['%s'] == 'pbmc3k'", "selectExampleData"),
|
|
| 164 |
- h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 165 |
- "Data was loaded with the 'TENxPBMCData' package.", |
|
| 166 |
- tags$br(), |
|
| 167 |
- tags$br() |
|
| 168 |
- ), |
|
| 169 |
- conditionalPanel( |
|
| 170 |
- condition = sprintf("input['%s'] == 'pbmc4k'", "selectExampleData"),
|
|
| 171 |
- h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "4,430 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 172 |
- "Data was loaded with the 'TENxPBMCData' package.", |
|
| 173 |
- tags$br(), |
|
| 174 |
- tags$br() |
|
| 175 |
- ), |
|
| 176 |
- conditionalPanel( |
|
| 177 |
- condition = sprintf("input['%s'] == 'pbmc6k'", "selectExampleData"),
|
|
| 178 |
- h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "5,419 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 179 |
- "Data was loaded with the 'TENxPBMCData' package.", |
|
| 180 |
- tags$br(), |
|
| 181 |
- tags$br() |
|
| 182 |
- ), |
|
| 183 |
- conditionalPanel( |
|
| 184 |
- condition = sprintf("input['%s'] == 'pbmc8k'", "selectExampleData"),
|
|
| 185 |
- h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "8,381 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 186 |
- "Data was loaded with the 'TENxPBMCData' package.", |
|
| 187 |
- tags$br(), |
|
| 188 |
- tags$br() |
|
| 144 |
+ ) |
|
| 145 |
+ ), |
|
| 146 |
+ actionButton("addFilesImport", "Add To Dataset List")
|
|
| 189 | 147 |
), |
| 190 | 148 |
conditionalPanel( |
| 191 |
- condition = sprintf("input['%s'] == 'pbmc33k'", "selectExampleData"),
|
|
| 192 |
- h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "33,148 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 193 |
- "Data was loaded with the 'TENxPBMCData' package.", |
|
| 194 |
- tags$br(), |
|
| 195 |
- tags$br() |
|
| 149 |
+ condition = sprintf("input['%s'] == 'example'", "uploadChoice"),
|
|
| 150 |
+ h3("Choose Example Dataset:"),
|
|
| 151 |
+ selectInput("selectExampleData", label = NULL, exampleDatasets),
|
|
| 152 |
+ conditionalPanel( |
|
| 153 |
+ condition = sprintf("input['%s'] == 'fluidigm_pollen'", "selectExampleData"),
|
|
| 154 |
+ h3(tags$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")), |
|
| 155 |
+ "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.", |
|
| 156 |
+ tags$br(), |
|
| 157 |
+ tags$br() |
|
| 158 |
+ ), |
|
| 159 |
+ conditionalPanel( |
|
| 160 |
+ condition = sprintf("input['%s'] == 'allen_tasic'", "selectExampleData"),
|
|
| 161 |
+ h3(tags$a(href = "http://dx.doi.org/10.1038/nn.4216", "Mouse visual cortex cells from (Tasic et al. 2016)", target = "_blank")), |
|
| 162 |
+ "Subset of 379 cells from the mouse visual cortex. Data was loaded from the 'scRNASeq' package.", |
|
| 163 |
+ tags$br(), |
|
| 164 |
+ tags$br() |
|
| 165 |
+ ), |
|
| 166 |
+ conditionalPanel( |
|
| 167 |
+ condition = sprintf("input['%s'] == 'NestorowaHSCData'", "selectExampleData"),
|
|
| 168 |
+ h3(tags$a(href = "https://www.nature.com/articles/nbt.2967", "1920 Mouse haematopoietic stem cells from (Nestorowa et al. 2015).", target= "_blank")), |
|
| 169 |
+ "Data was loaded from the 'scRNASeq' package.", |
|
| 170 |
+ tags$br(), |
|
| 171 |
+ tags$br() |
|
| 172 |
+ ), |
|
| 173 |
+ conditionalPanel( |
|
| 174 |
+ condition = sprintf("input['%s'] == 'pbmc3k'", "selectExampleData"),
|
|
| 175 |
+ h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 176 |
+ "Data was loaded with the 'TENxPBMCData' package.", |
|
| 177 |
+ tags$br(), |
|
| 178 |
+ tags$br() |
|
| 179 |
+ ), |
|
| 180 |
+ conditionalPanel( |
|
| 181 |
+ condition = sprintf("input['%s'] == 'pbmc4k'", "selectExampleData"),
|
|
| 182 |
+ h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "4,430 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 183 |
+ "Data was loaded with the 'TENxPBMCData' package.", |
|
| 184 |
+ tags$br(), |
|
| 185 |
+ tags$br() |
|
| 186 |
+ ), |
|
| 187 |
+ conditionalPanel( |
|
| 188 |
+ condition = sprintf("input['%s'] == 'pbmc6k'", "selectExampleData"),
|
|
| 189 |
+ h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "5,419 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 190 |
+ "Data was loaded with the 'TENxPBMCData' package.", |
|
| 191 |
+ tags$br(), |
|
| 192 |
+ tags$br() |
|
| 193 |
+ ), |
|
| 194 |
+ conditionalPanel( |
|
| 195 |
+ condition = sprintf("input['%s'] == 'pbmc8k'", "selectExampleData"),
|
|
| 196 |
+ h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "8,381 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 197 |
+ "Data was loaded with the 'TENxPBMCData' package.", |
|
| 198 |
+ tags$br(), |
|
| 199 |
+ tags$br() |
|
| 200 |
+ ), |
|
| 201 |
+ conditionalPanel( |
|
| 202 |
+ condition = sprintf("input['%s'] == 'pbmc33k'", "selectExampleData"),
|
|
| 203 |
+ h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "33,148 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 204 |
+ "Data was loaded with the 'TENxPBMCData' package.", |
|
| 205 |
+ tags$br(), |
|
| 206 |
+ tags$br() |
|
| 207 |
+ ), |
|
| 208 |
+ conditionalPanel( |
|
| 209 |
+ condition = sprintf("input['%s'] == 'pbmc68k'", "selectExampleData"),
|
|
| 210 |
+ h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "68,579 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 211 |
+ "Data was loaded with the 'TENxPBMCData' package.", |
|
| 212 |
+ tags$br(), |
|
| 213 |
+ tags$br() |
|
| 214 |
+ ), |
|
| 215 |
+ actionButton("addExampleImport", "Add To Sample List")
|
|
| 196 | 216 |
), |
| 197 | 217 |
conditionalPanel( |
| 198 |
- condition = sprintf("input['%s'] == 'pbmc68k'", "selectExampleData"),
|
|
| 199 |
- h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "68,579 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")), |
|
| 200 |
- "Data was loaded with the 'TENxPBMCData' package.", |
|
| 201 |
- tags$br(), |
|
| 202 |
- tags$br() |
|
| 203 |
- ), |
|
| 204 |
- actionButton("addExampleImport", "Add To Sample List")
|
|
| 205 |
- ), |
|
| 206 |
- conditionalPanel( |
|
| 207 |
- condition = sprintf("input['%s'] == 'rds'", "uploadChoice"),
|
|
| 208 |
- h3("2. Choose an RDS file that contains a SingleCellExperiment or Seurat object:"),
|
|
| 209 |
- fileInput( |
|
| 210 |
- "rdsFile", "SingleCellExperiment or Seurat RDS file:", accept = c(".rds", ".RDS")
|
|
| 211 |
- ), |
|
| 212 |
- actionButton("addRDSImport", "Add To Sample List")
|
|
| 213 |
- ), |
|
| 214 |
- conditionalPanel( |
|
| 215 |
- condition = sprintf("input['%s'] == 'directory'", "uploadChoice"),
|
|
| 216 |
- tags$style(HTML("
|
|
| 217 |
- div {
|
|
| 218 |
- word-wrap: break-word; |
|
| 219 |
- } |
|
| 220 |
- ")), |
|
| 221 |
- h3("2. Choose a Preprocessing Tool:"),
|
|
| 222 |
- radioButtons("algoChoice", label = NULL, c("Cell Ranger v2" = "cellRanger2",
|
|
| 223 |
- "Cell Ranger v3" = "cellRanger3", |
|
| 224 |
- "STARsolo" = "starSolo", |
|
| 225 |
- "BUStools" = "busTools", |
|
| 226 |
- "SEQC" = "seqc", |
|
| 227 |
- "Optimus" = "optimus") |
|
| 218 |
+ condition = sprintf("input['%s'] == 'rds'", "uploadChoice"),
|
|
| 219 |
+ h3("Choose an RDS file that contains a SingleCellExperiment or Seurat object:"),
|
|
| 220 |
+ fileInput( |
|
| 221 |
+ "rdsFile", "SingleCellExperiment or Seurat RDS file:", accept = c(".rds", ".RDS")
|
|
| 222 |
+ ), |
|
| 223 |
+ actionButton("addRDSImport", "Add To Sample List")
|
|
| 228 | 224 |
), |
| 229 |
- tags$br(), |
|
| 225 |
+ #conditionalPanel( |
|
| 226 |
+ #condition = sprintf("input['%s'] == 'directory'", "uploadChoice"),
|
|
| 227 |
+ #tags$style(HTML("
|
|
| 228 |
+ #div {
|
|
| 229 |
+ # word-wrap: break-word; |
|
| 230 |
+ #} |
|
| 231 |
+ #")), |
|
| 232 |
+ #h3("2. Choose a Preprocessing Tool:"),
|
|
| 233 |
+ #radioButtons("algoChoice", label = NULL, c("Cell Ranger v2" = "cellRanger2",
|
|
| 234 |
+ # "Cell Ranger v3" = "cellRanger3", |
|
| 235 |
+ # "STARsolo" = "starSolo", |
|
| 236 |
+ # "BUStools" = "busTools", |
|
| 237 |
+ # "SEQC" = "seqc", |
|
| 238 |
+ # "Optimus" = "optimus") |
|
| 239 |
+ #), |
|
| 240 |
+ #tags$br(), |
|
| 230 | 241 |
conditionalPanel( |
| 231 |
- condition = sprintf("input['%s'] == 'cellRanger2'", "algoChoice"),
|
|
| 242 |
+ condition = sprintf("input['%s'] == 'cellRanger2'", "uploadChoice"),
|
|
| 232 | 243 |
actionButton("addCR2Sample", "Add a Sample"),
|
| 233 | 244 |
), |
| 234 | 245 |
conditionalPanel( |
| 235 |
- condition = sprintf("input['%s'] == 'cellRanger3'", "algoChoice"),
|
|
| 246 |
+ condition = sprintf("input['%s'] == 'cellRanger3'", "uploadChoice"),
|
|
| 236 | 247 |
actionButton("addCR3Sample", "Add a Sample"),
|
| 237 | 248 |
), |
| 238 | 249 |
conditionalPanel( |
| 239 |
- condition = sprintf("input['%s'] == 'starSolo'", "algoChoice"),
|
|
| 250 |
+ condition = sprintf("input['%s'] == 'starSolo'", "uploadChoice"),
|
|
| 240 | 251 |
wellPanel( |
| 241 | 252 |
h5("Please select the directory that contains your /Gene directory as your base directory. ")
|
| 242 | 253 |
), |
| 243 | 254 |
actionButton("addSSSample", "Add a Sample"),
|
| 244 | 255 |
), |
| 245 | 256 |
conditionalPanel( |
| 246 |
- condition = sprintf("input['%s'] == 'busTools'", "algoChoice"),
|
|
| 257 |
+ condition = sprintf("input['%s'] == 'busTools'", "uploadChoice"),
|
|
| 247 | 258 |
wellPanel( |
| 248 | 259 |
h5("Please select your /genecount directory as your base directory.")
|
| 249 | 260 |
), |
| 250 | 261 |
actionButton("addBUSSample", "Add a Sample"),
|
| 251 | 262 |
), |
| 252 | 263 |
conditionalPanel( |
| 253 |
- condition = sprintf("input['%s'] == 'seqc'", "algoChoice"),
|
|
| 264 |
+ condition = sprintf("input['%s'] == 'seqc'", "uploadChoice"),
|
|
| 254 | 265 |
wellPanel( |
| 255 | 266 |
h5("Please select the directory that contains your sample files as your base directory.")
|
| 256 | 267 |
), |
| 257 | 268 |
actionButton("addSEQSample", "Add a Sample"),
|
| 258 | 269 |
), |
| 259 | 270 |
conditionalPanel( |
| 260 |
- condition = sprintf("input['%s'] == 'optimus'", "algoChoice"),
|
|
| 271 |
+ condition = sprintf("input['%s'] == 'optimus'", "uploadChoice"),
|
|
| 261 | 272 |
wellPanel( |
| 262 | 273 |
h5("Please select the directory that contains the following four directories - call-MergeCountFiles, call-MergeCellMetrics, call-MergeGeneMetrics, call-RunEmptyDrops - as your base directory.")
|
| 263 | 274 |
), |
| 264 | 275 |
actionButton("addOptSample", "Add a Sample"),
|
| 265 | 276 |
), |
| 277 |
+ style = "primary" |
|
| 266 | 278 |
), |
| 267 |
- tags$hr(), |
|
| 268 |
- h3("3. Import:"),
|
|
| 269 |
- wellPanel( |
|
| 270 |
- h4("Samples to Import:"),
|
|
| 271 |
- fluidRow( |
|
| 272 |
- column(3, tags$b("Type")),
|
|
| 273 |
- column(3, tags$b("Location")),
|
|
| 274 |
- column(3, tags$b("Sample Name")),
|
|
| 275 |
- column(3, tags$b("Remove"))
|
|
| 279 |
+ |
|
| 280 |
+ bsCollapsePanel( |
|
| 281 |
+ "2. Create dataset:", |
|
| 282 |
+ wellPanel( |
|
| 283 |
+ h4("Samples to Import:"),
|
|
| 284 |
+ fluidRow( |
|
| 285 |
+ column(3, tags$b("Type")),
|
|
| 286 |
+ column(3, tags$b("Location")),
|
|
| 287 |
+ column(3, tags$b("Sample Name")),
|
|
| 288 |
+ column(3, tags$b("Remove"))
|
|
| 289 |
+ ), |
|
| 290 |
+ tags$div(id = "newSampleImport"), |
|
| 291 |
+ tags$br(), |
|
| 292 |
+ tags$br(), |
|
| 293 |
+ actionButton("clearAllImport", "Clear Samples")
|
|
| 294 |
+ ), |
|
| 295 |
+ shinyjs::hidden( |
|
| 296 |
+ tags$div( |
|
| 297 |
+ id = "combineOptions", |
|
| 298 |
+ radioButtons("combineSCEChoice", label = NULL, c("Add to existing dataset" = 'addToExistingSCE',
|
|
| 299 |
+ "Overwrite existing dataset" = "overwriteSCE") |
|
| 300 |
+ ) |
|
| 301 |
+ ) |
|
| 276 | 302 |
), |
| 277 |
- tags$div(id = "newSampleImport"), |
|
| 303 |
+ actionButton("uploadData", "Create"),
|
|
| 304 |
+ |
|
| 278 | 305 |
tags$br(), |
| 279 | 306 |
tags$br(), |
| 280 |
- actionButton("clearAllImport", "Clear Samples")
|
|
| 307 |
+ style = "primary" |
|
| 281 | 308 |
), |
| 282 |
- shinyjs::hidden( |
|
| 283 |
- tags$div( |
|
| 284 |
- id = "combineOptions", |
|
| 285 |
- radioButtons("combineSCEChoice", label = NULL, c("Add to existing SCE object" = 'addToExistingSCE',
|
|
| 286 |
- "Overwrite existing SCE object" = "overwriteSCE") |
|
| 309 |
+ |
|
| 310 |
+ bsCollapsePanel( |
|
| 311 |
+ "3. Data summary:", |
|
| 312 |
+ hidden( |
|
| 313 |
+ wellPanel( |
|
| 314 |
+ id = "annotationData", |
|
| 315 |
+ h3("Data summary"),
|
|
| 316 |
+ DT::dataTableOutput("summarycontents"),
|
|
| 317 |
+ |
|
| 318 |
+ tags$hr(), |
|
| 319 |
+ |
|
| 320 |
+ h3("Dataset options:"),
|
|
| 321 |
+ selectInput("importFeatureNamesOpt",
|
|
| 322 |
+ "Set feature ID (only showing annotations without the NAs)", |
|
| 323 |
+ c("Default", featureChoice)),
|
|
| 324 |
+ selectInput("importFeatureDispOpt",
|
|
| 325 |
+ "Set feature names to be displayed in downstream visualization", |
|
| 326 |
+ c("Default", featureChoice)),
|
|
| 327 |
+ |
|
| 328 |
+ withBusyIndicatorUI(actionButton("importFeatureDipSet", "Set")),
|
|
| 287 | 329 |
) |
| 288 |
- ) |
|
| 289 |
- ), |
|
| 290 |
- actionButton("uploadData", "Import"),
|
|
| 291 |
- |
|
| 292 |
- tags$br(), |
|
| 293 |
- tags$br(), |
|
| 294 |
- hidden( |
|
| 295 |
- wellPanel( |
|
| 296 |
- id = "annotationData", |
|
| 297 |
- h3("Data summary"),
|
|
| 298 |
- tableOutput("summarycontents"),
|
|
| 299 |
- |
|
| 300 |
- tags$hr(), |
|
| 301 |
- |
|
| 302 |
- h3("Set Feature for Display:"),
|
|
| 303 |
- selectInput("importFeatureDispOpt",
|
|
| 304 |
- "Select the feature ID type that should be displayed in downstream visualization", |
|
| 305 |
- c("Rownames (Default)", featureChoice)),
|
|
| 306 |
- withBusyIndicatorUI(actionButton("importFeatureDipSet", "Set")),
|
|
| 307 |
- ) |
|
| 308 |
- ), |
|
| 309 |
- |
|
| 310 |
- tags$div( |
|
| 311 |
- class = "container", |
|
| 312 |
- p("")
|
|
| 313 |
- ), |
|
| 314 |
- |
|
| 315 |
- nonLinearWorkflowUI(id = "nlw-import") |
|
| 316 |
- ) |
|
| 317 |
- #includeHTML("www/footer.html")
|
|
| 330 |
+ ), |
|
| 331 |
+ |
|
| 332 |
+ style = "primary" |
|
| 333 |
+ ) |
|
| 334 |
+ ), |
|
| 335 |
+ nonLinearWorkflowUI(id = "nlw-import") |
|
| 318 | 336 |
) |
| 319 | 337 |
|
