Nothing
tabPanel("Summary and Filter",
tabsetPanel(
tabPanel("Filtering",
br(),
sidebarLayout(
sidebarPanel(
br(),
selectInput("filter_type", "Select filter type", c("By Metadata", "By Samples", "By Microbes")),
# Filtering by metadata
conditionalPanel(condition = "input.filter_type == 'By Metadata'",
selectInput("select_condition_sample_filter_sidebar", "Select a variable", c("Reads", covariates)),
conditionalPanel(condition = "output.filter_type == 'num.continuous'",
helpText("Please select range of the feature to keep"),
numericInput("num_filter_min", "Min", 0),
numericInput("num_filter_max", "Max", 0),
withBusyIndicatorUI(
actionButton("filter_num", "Filter")
)
),
conditionalPanel(condition = "output.filter_type == 'cat'",
helpText("Please select levels of the feature to keep"),
uiOutput("filter_cat_options"),
withBusyIndicatorUI(
actionButton("filter_cat", "Filter")
)
)
),
# Filtering by sample
conditionalPanel(condition = "input.filter_type == 'By Samples'",
selectizeInput('filterSample', 'Choose sample name(s) for removal',
choices = sample.names.all, selected=NULL, multiple = TRUE),
withBusyIndicatorUI(
actionButton("filterSampleButton", "Filter")
)
),
# Filtering by microbes
conditionalPanel(condition = "input.filter_type == 'By Microbes'",
br(),
selectInput("filter_type_micro", "Select filter type",
c("By mapped read number",
"By relative abundace",
"By prevalence")
),
conditionalPanel(condition = "input.filter_type_micro == 'By mapped read number'",
helpText("Please select the average minimum read mapped"),
numericInput("read_filter_min_micro", "Min", 0, min = 0, max = 10000),
withBusyIndicatorUI(
actionButton("filter_read_micro", "Filter")
)
),
conditionalPanel(condition = "input.filter_type_micro == 'By relative abundace'",
helpText("Please select average minimum RA"),
numericInput("ra_filter_min_micro", "Min", 0, min = 0, max = 1),
withBusyIndicatorUI(
actionButton("filter_ra_micro", "Filter")
)
),
conditionalPanel(condition = "input.filter_type_micro == 'By prevalence'",
helpText("Please select minimum prevalence"),
numericInput("prev_filter_min", "Min", 0, min = 0, max = 1),
withBusyIndicatorUI(
actionButton("filter_prev_micro", "Filter")
)
)
),
br(),
withBusyIndicatorUI(
actionButton("reset_button", "Reset")
),
br(),
downloadButton('download_rds', 'Download (.rds)'),
width=3
),
mainPanel(
fluidRow(
column(6,
h4("Overall Summary Table", align="center"),
br(),
tableOutput("contents_summary")
),
column(6,
h4("Variable Summary Plots", align="center"),
br(),
plotlyOutput("summary_plot_top", height="300px"),
plotlyOutput("summary_plot_bottom", height="300px")
)
),
width=9
)
)
),
tabPanel("Categorize",
tags$br(),
sidebarLayout(
sidebarPanel(
selectizeInput('bin_cov', 'Covariate', choices=num_covariates, multiple=FALSE),
uiOutput("nbins"),
textInput('bin_breaks', 'Custom Breaks (Comma Delimited)'),
verbatimTextOutput("bin_to1"),
textInput('bin_labels', 'Custom Labels (Comma Delimited)'),
verbatimTextOutput("bin_to2"),
textInput("new_covariate", "Covariate Label", value = "new_cov"),
actionButton("create_bins", "Create Bins"),
width=5
),
mainPanel(
plotlyOutput("unbin_plot", height="200px"),
br(),
plotlyOutput("bin_plot"),
width=7
)
)
),
tabPanel("Read Counts & Relative Abundance",
br(),
sidebarLayout(
sidebarPanel(
br(),
selectizeInput('taxlTable', 'Taxonomy Level', choices = tax.name, selected='no rank'),
width=3
),
mainPanel(
tabsetPanel(
tabPanel("Relative Abundance",
br(),
DT::dataTableOutput("TaxRAtable", width='95%'),
downloadButton('downloadData', 'Download (.csv)')
),
tabPanel("Read Counts",
br(),
DT::dataTableOutput("TaxCountTable",width='95%'),
downloadButton('downloadCountData', 'Download (.csv)')
)
#coreOTUModuleUI("coreOTUModule")
),
width=9
)
)
)
)
)
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