Nothing
ui.page_repository <- function() {
tabPanel(
title = "Repository",
icon = icon("database"),
sidebarLayout(
sidebarPanel(
width = 3,
shinyWidgets::actionBttn(
inputId = "use_repository",
label = "How to use repository",
icon = icon("question-circle"),
style = "bordered",
color = "primary",
size = "sm"
),
shinyWidgets::prettyCheckboxGroup("hubs_text", "Active Data Hub:",
choiceNames = c(
"UCSC Public", "TCGA",
"GDC", "ICGC",
"Pan-Cancer Atlas", "TOIL",
"Treehouse", "PCAWG",
"ATAC-seq", "Single Cell"
),
choiceValues = c(
"publicHub", "tcgaHub", "gdcHub", "icgcHub", "pancanAtlasHub",
"toilHub", "treehouseHub", "pcawgHub", "atacseqHub", "singlecellHub"
),
selected = "gdcHub",
shape = "round",
status = "success",
animation = "tada"
),
shinyBS::bsPopover("hubs_text",
title = "Tips",
content = "Data hub/host is an individual database for storing genomic data",
placement = "right", options = list(container = "body")
),
uiOutput("cohorts_text"),
shinyBS::bsPopover("cohorts_text",
title = "Tips",
content = "Cohort is an independent study, it contains datasets with same patients",
placement = "right", options = list(container = "body")
),
shinyWidgets::prettyCheckboxGroup("type_text", "Data Type:",
choiceNames = c(
"Phenotype", "Genomic matrix\n(e.g., expression)",
"Genomic segments", "Mutations"
),
choiceValues = c("clinicalMatrix", "genomicMatrix", "genomicSegment", "mutationVector"),
selected = c("clinicalMatrix", "genomicMatrix", "genomicSegment", "mutationVector"),
status = "success",
animation = "tada"
),
shinyBS::bsPopover("type_text",
title = "Tips",
content = "Data type divide datasets into 4 basic categories: Phenotype for clinical or other phenotype data; Genomic matrix is a feature by sample matrix representing gene/probe expression matrix; Genomic segments for copy number records; Mutations for mutation annotations",
placement = "right", options = list(container = "body")
),
uiOutput("subtype_text"),
shinyBS::bsPopover("subtype_text",
title = "Tips",
content = "Subtype are categories based on biological meaning instead of storing format like Type",
placement = "right", options = list(container = "body")
)
),
mainPanel(
DT::dataTableOutput("xena_table"),
hr(),
fluidRow(
column(
offset = 1,
4,
actionBttn(
inputId = "show_met",
label = "Show Metadata",
style = "gradient",
# color = "danger",
icon = icon("database"),
size = "sm"
)
),
column(
4,
actionBttn(
inputId = "req_data",
label = "Request Data",
style = "gradient",
icon = icon("file"),
size = "sm"
)
),
column(
3,
actionBttn(
inputId = "analyze_data",
label = "Analyze Data",
style = "gradient",
icon = icon("chart-bar"),
size = "sm"
)
)
),
hr(),
shinyjs::hidden(
tags$div(
id = "show_data",
h4("Selected Data:", style = "font-size: 1.2em;font-weight: bold;margin-bottom: 5px;margin-top: 0;"),
h6("Wait until a table shows..."),
tableOutput(
"table"
)
)
)
)
)
)
}
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