inst/shiny/ui_01_import.R
In compbiomed/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",
"NestorowaHSC (Nestorowa et al, 2016)" = "NestorowaHSCData")
}
# User Interface for import Workflow ---
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 = paste0(docs.base, "index.html"),
"Read the docs.", target = "_blank")
)
)
),
tags$br(),
h1("Import"),
h5(tags$a(href = paste0(docs.artPath, "import_data.html"),
"(help)", target = "_blank")),
tags$hr(),
bsCollapse(
id = "importUI",
open = "1. Add sample to import:",
bsCollapsePanel(
"1. Add sample to import:",
radioButtons("uploadChoice", label = NULL, c("Cell Ranger (Version 3 or above)" = "cellRanger3",
# "Cell Ranger (Version 2)" = "cellRanger2",
"STARsolo" = "starSolo",
"BUStools" = "busTools",
"SEQC" = "seqc",
"Optimus" = "optimus",
#"Import from a preprocessing tool" = 'directory',
"Import from flat files (.csv, .txt, .mtx)" = "files",
"Upload SingleCellExperiment or Seurat object stored in an RDS File" = "rds",
"Import example datasets" = "example")
),
tags$hr(),
conditionalPanel(condition = sprintf("input['%s'] == 'files'", "uploadChoice"),
h4("Upload data in tab separated text format:"),
fluidRow(
column(width = 4,
wellPanel(
h5("Example count file:"),
HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
<th>Cell1</th><th>Cell2</th><th>…</th><th>CellN</th>
</tr></thead><tbody><tr class="odd"><td>Gene1</td><td>0</td>
<td>0</td><td>…</td><td>0</td></tr><tr class="even">
<td>Gene2</td><td>5</td><td>6</td><td>…</td><td>0</td>
</tr><tr class="odd"><td>Gene3</td><td>4</td><td>3</td>
<td>…</td><td>8</td></tr><tr class="even">
<td>…</td><td>…</td><td>…</td>
<td>…</td><td>…</td></tr><tr class="odd">
<td>GeneM</td><td>10</td><td>10</td><td>…</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(),
fileInput(
"countsfile",
HTML(
paste("Input assay (eg. counts, required):",
tags$span(style = "color:red", "*", sep = ""))
),
accept = c(
"text/csv", "text/comma-separated-values", "mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv"
)
)
),
h4("Input Assay Type:"),
selectInput("inputAssayType", label = NULL,
c("counts", "normcounts", "logcounts", "cpm",
"logcpm", "tpm", "logtpm")
)
),
column(width = 4,
wellPanel(
h5("Example cell annotation file:"),
HTML('<table class="table"><thead><tr class="header"><th>Cell</th>
<th>Annot1</th><th>…</th></tr></thead><tbody><tr class="odd">
<td>Cell1</td><td>a</td><td>…</td></tr><tr class="even">
<td>Cell2</td><td>a</td><td>…</td></tr><tr class="odd">
<td>Cell3</td><td>b</td><td>…</td></tr><tr class="even">
<td>…</td><td>…</td><td>…</td></tr><tr class="odd"><td>CellN</td>
<td>b</td><td>…</td></tr></tbody></table>'),
tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
"Download an example annotation file here.", target = "_blank"),
tags$br(),
fileInput(
"annotFile", "Cell annotations (optional):",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv"
)
)
)
),
column(width = 4,
wellPanel(
h5("Example feature file:"),
HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
<th>Annot2</th><th>…</th></tr></thead><tbody><tr class="odd">
<td>Gene1</td><td>a</td><td>…</td></tr><tr class="even">
<td>Gene2</td><td>a</td><td>…</td></tr><tr class="odd">
<td>Gene3</td><td>b</td><td>…</td></tr><tr class="even">
<td>…</td><td>…</td><td>…</td></tr><tr class="odd"><td>GeneM</td>
<td>b</td><td>…</td></tr></tbody></table>'),
tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
"Download an example feature file here.", target = "_blank"),
tags$br(),
fileInput(
"featureFile", "Feature annotations (optional):",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv"
)
)
)
)
),
actionButton("addFilesImport", "Add to dataset list")
),
conditionalPanel(
condition = sprintf("input['%s'] == 'example'", "uploadChoice"),
h4("Choose Example Dataset:"),
selectInput("selectExampleData", label = NULL, exampleDatasets, width = "340px"),
conditionalPanel(
condition = sprintf("input['%s'] == 'fluidigm_pollen'", "selectExampleData"),
h4(tags$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"),
h4(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$br()
),
conditionalPanel(
condition = sprintf("input['%s'] == 'NestorowaHSCData'", "selectExampleData"),
h4(tags$a(href = "https://www.nature.com/articles/nbt.2967", "1920 Mouse haematopoietic stem cells from (Nestorowa et al. 2015).", target= "_blank")),
"Data was loaded from the 'scRNASeq' package.",
tags$br(),
tags$br()
),
conditionalPanel(
condition = sprintf("input['%s'] == 'pbmc3k'", "selectExampleData"),
h4(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$br()
),
conditionalPanel(
condition = sprintf("input['%s'] == 'pbmc4k'", "selectExampleData"),
h4(tags$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"),
h4(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$br()
),
conditionalPanel(
condition = sprintf("input['%s'] == 'pbmc8k'", "selectExampleData"),
h4(tags$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"),
h4(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$br()
),
conditionalPanel(
condition = sprintf("input['%s'] == 'pbmc68k'", "selectExampleData"),
h4(tags$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"),
h4("Choose an RDS file that contains a SingleCellExperiment or Seurat object:"),
fileInput(
"rdsFile", "SingleCellExperiment or Seurat RDS file:", accept = c(".rds", ".RDS")
),
actionButton("addRDSImport", "Add to sample list")
),
#conditionalPanel(
#condition = sprintf("input['%s'] == 'directory'", "uploadChoice"),
#tags$style(HTML("
#div {
# word-wrap: break-word;
#}
#")),
#h3("2. Choose a Preprocessing Tool:"),
#radioButtons("algoChoice", label = NULL, c("Cell Ranger v2" = "cellRanger2",
# "Cell Ranger v3" = "cellRanger3",
# "STARsolo" = "starSolo",
# "BUStools" = "busTools",
# "SEQC" = "seqc",
# "Optimus" = "optimus")
#),
#tags$br(),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'cellRanger2'", "uploadChoice"),
# actionButton("addCR2Sample", "Add a sample"),
# ),
conditionalPanel(
condition = sprintf("input['%s'] == 'cellRanger3'", "uploadChoice"),
h4("Upload data for Cell Ranger:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Matrix file (e.g. matrix.mtx or matrix.mtx.gz):"),
fileInput(
"countsfile_custom", "Matrix file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
"Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Barcodes file (e.g. barcodes.tsv or barcodes.tsv.gz):"),
fileInput(
"annotFile_custom", "Barcodes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
"Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Features file (e.g. features.tsv or features.tsv.gz):"),
fileInput(
"featureFile_custom", "Features file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
"Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
h5("(OPTIONAL)"),
h5("Metrics Summary file (metrics_summary.csv):"),
fileInput(
"summaryFile_custom", "Summary file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = FALSE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
# "Download an example metrics_summary.csv file here.", target = "_blank")
)
)
),
textInput("sampleNameCR", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'starSolo'", "uploadChoice"),
# 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'] == 'starSolo'", "uploadChoice"),
h4("Upload data for starSolo:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Matrix file (e.g. matrix.mtx or matrix.mtx.gz):"),
fileInput(
"countsfile_custom_starSolo", "Matrix file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
"Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Barcodes file (e.g. barcodes.tsv or barcodes.tsv.gz):"),
fileInput(
"annotFile_custom_starSolo", "Barcodes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
"Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Features file (e.g. features.tsv or features.tsv.gz):"),
fileInput(
"featureFile_custom_starSolo", "Features file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
"Download an example features.tsv file here.", target = "_blank")
)
)
),
textInput("sampleNameSS", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom_starSolo", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'busTools'", "uploadChoice"),
# wellPanel(
# h5("Please select your /genecount directory as your base directory.")
# ),
# actionButton("addBUSSample", "Add a sample"),
# ),
conditionalPanel(
condition = sprintf("input['%s'] == 'busTools'", "uploadChoice"),
h4("Upload data for BUSTools:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Matrix file (e.g. matrix.mtx or matrix.mtx.gz):"),
fileInput(
"countsfile_custom_busTools", "Matrix file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
"Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Barcodes file (e.g. barcodes.tsv or barcodes.tsv.gz):"),
fileInput(
"annotFile_custom_busTools", "Barcodes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
"Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Features file (e.g. features.tsv or features.tsv.gz):"),
fileInput(
"featureFile_custom_busTools", "Features file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
"Download an example features.tsv file here.", target = "_blank")
)
)
),
textInput("sampleNameBT", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom_busTools", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'seqc'", "uploadChoice"),
# 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'] == 'seqc'", "uploadChoice"),
# 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'] == 'seqc'", "uploadChoice"),
h4("Upload data for SEQC:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Read counts file (e.g. pbmc_1k_sparse_read_counts.mtx or pbmc_1k_sparse_read_counts.mtx.gz:"),
fileInput(
"readCounts_custom_seqc", "Read counts file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
# "Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Molecule counts file (e.g. pbmc_1k_sparse_molecule_counts.mtx or pbmc_1k_sparse_molecule_counts.mtx.gz):"),
fileInput(
"moleculeCounts_custom_seqc", "Molecule counts file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
# "Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Barcodes file (e.g. pbmc_1k_sparse_counts_barcodes.csv):"),
fileInput(
"barcodes_custom_seqc", "Barcodes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Genes file (e.g. pbmc_1k_sparse_counts_genes.csv):"),
fileInput(
"genes_custom_seqc", "Genes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
)
),
textInput("sampleNameSC", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom_seqc", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
conditionalPanel(
condition = sprintf("input['%s'] == 'optimus'", "uploadChoice"),
h4("Upload data for Optimus:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Counts file (e.g. sparse_counts.npz):"),
fileInput(
"matrix_custom_optimus", "Counts file:",
accept = c(
"text/csv", "text/comma-separated-values", ".npz",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
# "Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Column index file (e.g. sparse_counts_col_index.npy):"),
fileInput(
"colIndex_custom_optimus", "Column index file:",
accept = c(
"text/csv", "text/comma-separated-values", ".npy",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
# "Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Row index file (e.g. sparse_counts_row_index.npy):"),
fileInput(
"rowIndex_custom_optimus", "Row index file:",
accept = c(
"text/csv", "text/comma-separated-values", ".npy",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Cell metrics file (e.g. merged-cell-metrics.csv or merged-cell-metrics.csv.gz):"),
fileInput(
"cellMetrics_custom_optimus", "Cell metrics file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Gene metrics file (e.g. merged-gene-metrics.csv or merged-gene-metrics.csv.gz):"),
fileInput(
"geneMetrics_custom_optimus", "Gene metrics file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Empty drops file (e.g. empty_drops_result.csv):"),
fileInput(
"emptyDrops_custom_optimus", "Empty drops file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
)
),
textInput("sampleNameOP", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom_optimus", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'optimus'", "uploadChoice"),
# 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"),
# ),
style = "primary"
),
bsCollapsePanel(
"2. Create dataset:",
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$br(),
actionButton("clearAllImport", "Clear Samples")
),
shinyjs::hidden(
tags$div(
id = "combineOptions",
radioButtons("combineSCEChoice", label = NULL, c("Add to existing dataset" = 'addToExistingSCE',
"Overwrite existing dataset" = "overwriteSCE")
)
)
),
column(
12,
fluidRow(
actionButton("uploadData", "Import"),
actionButton("backToStepOne", "Add one more sample")
)
),
style = "primary"
),
bsCollapsePanel(
"3. Data summary:",
hidden(
wellPanel(
id = "annotationData",
h3("Data summary"),
DT::dataTableOutput("summarycontents"),
tags$hr(),
h3("Dataset options:"),
selectInput("importFeatureNamesOpt",
"Set feature ID (only showing annotations without the NAs)",
c("Default", featureChoice)),
selectInput("importFeatureDispOpt",
"Set feature names to be displayed in downstream visualization",
c("Default", featureChoice)),
withBusyIndicatorUI(actionButton("importFeatureDipSet", "Set")),
)
),
style = "primary"
)
),
nonLinearWorkflowUI(id = "nlw-import")
)
compbiomed/singleCellTK documentation built on May 8, 2024, 6:58 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
exampleDatasets <- c() ## Need to add final small example data here
if ("TENxPBMCData" %in% rownames(installed.packages())){
exampleDatasets <- c(exampleDatasets,
"PBMC 3K (10X)" = "pbmc3k",
"PBMC 4K (10X)" = "pbmc4k",
"PBMC 6K (10X)" = "pbmc6k",
"PBMC 8K (10X)" = "pbmc8k",
"PBMC 33K (10X)" = "pbmc33k",
"PBMC 68K (10X)" = "pbmc68k")
}
if ("scRNAseq" %in% rownames(installed.packages())){
exampleDatasets <- c(exampleDatasets,
"Fluidigm (Pollen et al, 2014)" = "fluidigm_pollen",
"Mouse Brain (Tasic et al, 2016)" = "allen_tasic",
"NestorowaHSC (Nestorowa et al, 2016)" = "NestorowaHSCData")
}
# User Interface for import Workflow ---
shinyPanelImport <- fluidPage(
useShinyjs(),
tags$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$a(href = paste0(docs.base, "index.html"),
"Read the docs.", target = "_blank")
)
)
),
tags$br(),
h1("Import"),
h5(tags$a(href = paste0(docs.artPath, "import_data.html"),
"(help)", target = "_blank")),
tags$hr(),
bsCollapse(
id = "importUI",
open = "1. Add sample to import:",
bsCollapsePanel(
"1. Add sample to import:",
radioButtons("uploadChoice", label = NULL, c("Cell Ranger (Version 3 or above)" = "cellRanger3",
# "Cell Ranger (Version 2)" = "cellRanger2",
"STARsolo" = "starSolo",
"BUStools" = "busTools",
"SEQC" = "seqc",
"Optimus" = "optimus",
#"Import from a preprocessing tool" = 'directory',
"Import from flat files (.csv, .txt, .mtx)" = "files",
"Upload SingleCellExperiment or Seurat object stored in an RDS File" = "rds",
"Import example datasets" = "example")
),
tags$hr(),
conditionalPanel(condition = sprintf("input['%s'] == 'files'", "uploadChoice"),
h4("Upload data in tab separated text format:"),
fluidRow(
column(width = 4,
wellPanel(
h5("Example count file:"),
HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
<th>Cell1</th><th>Cell2</th><th>…</th><th>CellN</th>
</tr></thead><tbody><tr class="odd"><td>Gene1</td><td>0</td>
<td>0</td><td>…</td><td>0</td></tr><tr class="even">
<td>Gene2</td><td>5</td><td>6</td><td>…</td><td>0</td>
</tr><tr class="odd"><td>Gene3</td><td>4</td><td>3</td>
<td>…</td><td>8</td></tr><tr class="even">
<td>…</td><td>…</td><td>…</td>
<td>…</td><td>…</td></tr><tr class="odd">
<td>GeneM</td><td>10</td><td>10</td><td>…</td><td>10</td>
</tr></tbody></table>'),
tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
"Download an example count file here.", target = "_blank"),
tags$br(),
fileInput(
"countsfile",
HTML(
paste("Input assay (eg. counts, required):",
tags$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(
h5("Example cell annotation file:"),
HTML('<table class="table"><thead><tr class="header"><th>Cell</th>
<th>Annot1</th><th>…</th></tr></thead><tbody><tr class="odd">
<td>Cell1</td><td>a</td><td>…</td></tr><tr class="even">
<td>Cell2</td><td>a</td><td>…</td></tr><tr class="odd">
<td>Cell3</td><td>b</td><td>…</td></tr><tr class="even">
<td>…</td><td>…</td><td>…</td></tr><tr class="odd"><td>CellN</td>
<td>b</td><td>…</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(),
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(
h5("Example feature file:"),
HTML('<table class="table"><thead><tr class="header"><th>Gene</th>
<th>Annot2</th><th>…</th></tr></thead><tbody><tr class="odd">
<td>Gene1</td><td>a</td><td>…</td></tr><tr class="even">
<td>Gene2</td><td>a</td><td>…</td></tr><tr class="odd">
<td>Gene3</td><td>b</td><td>…</td></tr><tr class="even">
<td>…</td><td>…</td><td>…</td></tr><tr class="odd"><td>GeneM</td>
<td>b</td><td>…</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(),
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 dataset list")
),
conditionalPanel(
condition = sprintf("input['%s'] == 'example'", "uploadChoice"),
h4("Choose Example Dataset:"),
selectInput("selectExampleData", label = NULL, exampleDatasets, width = "340px"),
conditionalPanel(
condition = sprintf("input['%s'] == 'fluidigm_pollen'", "selectExampleData"),
h4(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$br()
),
conditionalPanel(
condition = sprintf("input['%s'] == 'allen_tasic'", "selectExampleData"),
h4(tags$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'] == 'NestorowaHSCData'", "selectExampleData"),
h4(tags$a(href = "https://www.nature.com/articles/nbt.2967", "1920 Mouse haematopoietic stem cells from (Nestorowa et al. 2015).", target= "_blank")),
"Data was loaded from the 'scRNASeq' package.",
tags$br(),
tags$br()
),
conditionalPanel(
condition = sprintf("input['%s'] == 'pbmc3k'", "selectExampleData"),
h4(tags$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"),
h4(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$br()
),
conditionalPanel(
condition = sprintf("input['%s'] == 'pbmc6k'", "selectExampleData"),
h4(tags$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"),
h4(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$br()
),
conditionalPanel(
condition = sprintf("input['%s'] == 'pbmc33k'", "selectExampleData"),
h4(tags$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"),
h4(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$br()
),
actionButton("addExampleImport", "Add to sample list")
),
conditionalPanel(
condition = sprintf("input['%s'] == 'rds'", "uploadChoice"),
h4("Choose an RDS file that contains a SingleCellExperiment or Seurat object:"),
fileInput(
"rdsFile", "SingleCellExperiment or Seurat RDS file:", accept = c(".rds", ".RDS")
),
actionButton("addRDSImport", "Add to sample list")
),
#conditionalPanel(
#condition = sprintf("input['%s'] == 'directory'", "uploadChoice"),
#tags$style(HTML("
#div {
# word-wrap: break-word;
#}
#")),
#h3("2. 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$br(),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'cellRanger2'", "uploadChoice"),
# actionButton("addCR2Sample", "Add a sample"),
# ),
conditionalPanel(
condition = sprintf("input['%s'] == 'cellRanger3'", "uploadChoice"),
h4("Upload data for Cell Ranger:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Matrix file (e.g. matrix.mtx or matrix.mtx.gz):"),
fileInput(
"countsfile_custom", "Matrix file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
"Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Barcodes file (e.g. barcodes.tsv or barcodes.tsv.gz):"),
fileInput(
"annotFile_custom", "Barcodes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
"Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Features file (e.g. features.tsv or features.tsv.gz):"),
fileInput(
"featureFile_custom", "Features file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
"Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
h5("(OPTIONAL)"),
h5("Metrics Summary file (metrics_summary.csv):"),
fileInput(
"summaryFile_custom", "Summary file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = FALSE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
# "Download an example metrics_summary.csv file here.", target = "_blank")
)
)
),
textInput("sampleNameCR", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'starSolo'", "uploadChoice"),
# wellPanel(
# h5("Please select the directory that contains your /Gene directory as your base directory. ")
# ),
# actionButton("addSSSample", "Add a sample"),
# ),
conditionalPanel(
condition = sprintf("input['%s'] == 'starSolo'", "uploadChoice"),
h4("Upload data for starSolo:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Matrix file (e.g. matrix.mtx or matrix.mtx.gz):"),
fileInput(
"countsfile_custom_starSolo", "Matrix file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
"Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Barcodes file (e.g. barcodes.tsv or barcodes.tsv.gz):"),
fileInput(
"annotFile_custom_starSolo", "Barcodes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
"Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Features file (e.g. features.tsv or features.tsv.gz):"),
fileInput(
"featureFile_custom_starSolo", "Features file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
"Download an example features.tsv file here.", target = "_blank")
)
)
),
textInput("sampleNameSS", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom_starSolo", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'busTools'", "uploadChoice"),
# wellPanel(
# h5("Please select your /genecount directory as your base directory.")
# ),
# actionButton("addBUSSample", "Add a sample"),
# ),
conditionalPanel(
condition = sprintf("input['%s'] == 'busTools'", "uploadChoice"),
h4("Upload data for BUSTools:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Matrix file (e.g. matrix.mtx or matrix.mtx.gz):"),
fileInput(
"countsfile_custom_busTools", "Matrix file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
"Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Barcodes file (e.g. barcodes.tsv or barcodes.tsv.gz):"),
fileInput(
"annotFile_custom_busTools", "Barcodes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
"Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Features file (e.g. features.tsv or features.tsv.gz):"),
fileInput(
"featureFile_custom_busTools", "Features file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
),
tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
"Download an example features.tsv file here.", target = "_blank")
)
)
),
textInput("sampleNameBT", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom_busTools", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'seqc'", "uploadChoice"),
# wellPanel(
# h5("Please select the directory that contains your sample files as your base directory.")
# ),
# actionButton("addSEQSample", "Add a sample"),
# ),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'seqc'", "uploadChoice"),
# wellPanel(
# h5("Please select the directory that contains your sample files as your base directory.")
# ),
# actionButton("addSEQSample", "Add a sample"),
# ),
conditionalPanel(
condition = sprintf("input['%s'] == 'seqc'", "uploadChoice"),
h4("Upload data for SEQC:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Read counts file (e.g. pbmc_1k_sparse_read_counts.mtx or pbmc_1k_sparse_read_counts.mtx.gz:"),
fileInput(
"readCounts_custom_seqc", "Read counts file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
# "Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Molecule counts file (e.g. pbmc_1k_sparse_molecule_counts.mtx or pbmc_1k_sparse_molecule_counts.mtx.gz):"),
fileInput(
"moleculeCounts_custom_seqc", "Molecule counts file:",
accept = c(
"text/csv", "text/comma-separated-values", ".mtx",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
# "Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Barcodes file (e.g. pbmc_1k_sparse_counts_barcodes.csv):"),
fileInput(
"barcodes_custom_seqc", "Barcodes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Genes file (e.g. pbmc_1k_sparse_counts_genes.csv):"),
fileInput(
"genes_custom_seqc", "Genes file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
)
),
textInput("sampleNameSC", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom_seqc", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
conditionalPanel(
condition = sprintf("input['%s'] == 'optimus'", "uploadChoice"),
h4("Upload data for Optimus:"),
h5("Select matrix, barcodes and feature files for a sample using the file selectors below:"),
fluidRow(
column(width = 4,
wellPanel(
tags$b("Counts file (e.g. sparse_counts.npz):"),
fileInput(
"matrix_custom_optimus", "Counts file:",
accept = c(
"text/csv", "text/comma-separated-values", ".npz",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",
# "Download an example matrix.mtx file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Column index file (e.g. sparse_counts_col_index.npy):"),
fileInput(
"colIndex_custom_optimus", "Column index file:",
accept = c(
"text/csv", "text/comma-separated-values", ".npy",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",
# "Download an example barcodes.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Row index file (e.g. sparse_counts_row_index.npy):"),
fileInput(
"rowIndex_custom_optimus", "Row index file:",
accept = c(
"text/csv", "text/comma-separated-values", ".npy",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Cell metrics file (e.g. merged-cell-metrics.csv or merged-cell-metrics.csv.gz):"),
fileInput(
"cellMetrics_custom_optimus", "Cell metrics file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Gene metrics file (e.g. merged-gene-metrics.csv or merged-gene-metrics.csv.gz):"),
fileInput(
"geneMetrics_custom_optimus", "Gene metrics file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
),
column(width = 4,
wellPanel(
tags$b("Empty drops file (e.g. empty_drops_result.csv):"),
fileInput(
"emptyDrops_custom_optimus", "Empty drops file:",
accept = c(
"text/csv", "text/comma-separated-values",
"text/tab-separated-values", "text/plain", ".csv", ".tsv", ".gz"
),
multiple = TRUE
)
# ,
# tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",
# "Download an example features.tsv file here.", target = "_blank")
)
)
),
textInput("sampleNameOP", "Name for this sample:", value = "sample", placeholder = "sample"),
tags$h5("Note: Each sample should be given a unique name", style = "color: red;"),
actionButton("addFilesImport_custom_optimus", "Add to dataset list")
#actionButton("addCR3Sample", "Add a sample"),
),
# conditionalPanel(
# condition = sprintf("input['%s'] == 'optimus'", "uploadChoice"),
# wellPanel(
# h5("Please select the directory that contains the following four directories - call-MergeCountFiles, call-MergeCellMetrics, call-MergeGeneMetrics, call-RunEmptyDrops - as your base directory.")
# ),
# actionButton("addOptSample", "Add a sample"),
# ),
style = "primary"
),
bsCollapsePanel(
"2. Create dataset:",
wellPanel(
h4("Samples to Import:"),
fluidRow(
column(3, tags$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")
),
shinyjs::hidden(
tags$div(
id = "combineOptions",
radioButtons("combineSCEChoice", label = NULL, c("Add to existing dataset" = 'addToExistingSCE',
"Overwrite existing dataset" = "overwriteSCE")
)
)
),
column(
12,
fluidRow(
actionButton("uploadData", "Import"),
actionButton("backToStepOne", "Add one more sample")
)
),
style = "primary"
),
bsCollapsePanel(
"3. Data summary:",
hidden(
wellPanel(
id = "annotationData",
h3("Data summary"),
DT::dataTableOutput("summarycontents"),
tags$hr(),
h3("Dataset options:"),
selectInput("importFeatureNamesOpt",
"Set feature ID (only showing annotations without the NAs)",
c("Default", featureChoice)),
selectInput("importFeatureDispOpt",
"Set feature names to be displayed in downstream visualization",
c("Default", featureChoice)),
withBusyIndicatorUI(actionButton("importFeatureDipSet", "Set")),
)
),
style = "primary"
)
),
nonLinearWorkflowUI(id = "nlw-import")
)
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