tabPanel("Summary and Filter",
tabsetPanel(
tabPanel("Filter",
br(),
sidebarLayout(
sidebarPanel(
# View Style
selectInput("filter_type", "Filter By", c("Metadata", "Microbes")),
# Metadata
conditionalPanel(condition = "input.filter_type == 'Metadata'",
selectizeInput('filter_type_metadata', 'Select a Condition', choices=covariates, multiple=FALSE),
uiOutput("filter_metadata_params"),
withBusyIndicatorUI(
actionButton("filter_metadata_btn", "Filter", class = "btn-primary")
)
),
# Microbes
conditionalPanel(condition = "input.filter_type == 'Microbes'",
selectInput("filter_type_microbes", "Select Filter Condition", c("Average Read Number",
"Average Relative Abundance",
"Average Prevalence")
)
),
conditionalPanel(condition = "input.filter_type == 'Microbes' & input.filter_type_microbes == 'Average Read Number'",
numericInput("filter_microbes_read_inp", "Set Minimum", 0, min = 0, max = 10000),
withBusyIndicatorUI(
actionButton("filter_microbes_read_btn", "Filter", class = "btn-primary")
)
),
conditionalPanel(condition = "input.filter_type == 'Microbes' & input.filter_type_microbes == 'Average Relative Abundance'",
numericInput("filter_microbes_rela_min_inp", "Set Minimum", 0, min = 0, max = 1),
numericInput("filter_microbes_rela_max_inp", "Set Maximum", 1, min = 0, max = 1),
withBusyIndicatorUI(
actionButton("filter_microbes_rela_btn", "Filter", class = "btn-primary")
)
),
conditionalPanel(condition = "input.filter_type == 'Microbes' & input.filter_type_microbes == 'Average Prevalence'",
numericInput("filter_microbes_prev_min_inp", "Set Minimum", 0, min = 0, max = 1),
numericInput("filter_microbes_prev_max_inp", "Set Maximum", 1, min = 0, max = 1),
withBusyIndicatorUI(
actionButton("filter_microbes_prev_btn", "Filter", class = "btn-primary")
)
),
br(),
# Reset
withBusyIndicatorUI(
actionButton("filter_reset_btn", "Reset")
),
width=5,
br(),
downloadButton('download_rds', 'Download Animalcules File'),
br(),
downloadButton('download_biom', 'Download Biom File'),
checkboxInput("filter_adv", "Advanced Options"),
conditionalPanel(
condition = "input.filter_adv == true | input.global_adv == true",
# Discard samples
selectizeInput("filter_sample_dis", "Discard Samples", choices=sam.name, multiple=TRUE),
# Discard organisms
selectizeInput("filter_organism_dis", "Discard Organisms", choices=org.name, multiple=TRUE),
withBusyIndicatorUI(
actionButton("filter_discard_btn", "Discard")
)
),
br()
),
mainPanel(
fluidRow(
column(5,
tableOutput("filter_summary_table")
),
column(7,
plotlyOutput("filter_summary_top_plot", height="350px"),
plotlyOutput("filter_summary_bottom_plot", height="350px")
)
),
width=7
)
)
),
tabPanel("Categorize",
tags$br(),
sidebarLayout(
sidebarPanel(
selectizeInput('filter_bin_cov', 'Continuous Variables', choices=num_covariates, multiple=FALSE),
uiOutput("filter_nbins"),
textInput("filter_new_covariate", "New Variable Label", value = "new_var"),
checkboxInput("filter_bin_adv", "Advanced Options"),
conditionalPanel(
condition = "input.filter_bin_adv == true | input.global_adv == true",
textInput('filter_bin_breaks', 'Custom Breaks (Comma Delimited)'),
verbatimTextOutput("filter_bin_to1"),
textInput('filter_bin_labels', 'Custom Labels (Comma Delimited)'),
verbatimTextOutput("filter_bin_to2")
),
actionButton("filter_create_bins", "Create Bins", class = "btn-primary"),
width=5
),
mainPanel(
plotlyOutput("filter_unbin_plot", height="200px"),
br(),
plotlyOutput("filter_bin_plot"),
width=7
)
)
),
tabPanel("Assay Dashboard",
br(),
sidebarLayout(
sidebarPanel(
selectInput("select_assay", "Select Assay",
c("Count table" = "count",
"Relative Abundance table" = "ra",
"LogCPM table" = "logcpm",
"Taxonomy table" = "tax",
"Annotation table" = "annot"
)),
conditionalPanel(condition = sprintf("input['%s'] == 'count'", "select_assay"),
selectizeInput("assay_count_taxlev", "Tax Level", choices=tax.name, selected=tax.default),
actionButton("view_assay_count",
"View",
class = "btn-primary"),
downloadButton('download_assay_count', 'Download')
),
conditionalPanel(condition = sprintf("input['%s'] == 'ra'", "select_assay"),
selectizeInput("assay_ra_taxlev", "Tax Level", choices=tax.name, selected=tax.default),
actionButton("view_assay_ra",
"View",
class = "btn-primary"),
downloadButton('download_assay_ra', 'Download')
),
conditionalPanel(condition = sprintf("input['%s'] == 'logcpm'", "select_assay"),
selectizeInput("assay_logcpm_taxlev", "Tax Level", choices=tax.name, selected=tax.default),
actionButton("view_assay_logcpm",
"View",
class = "btn-primary"),
downloadButton('download_assay_logcpm', 'Download')
),
conditionalPanel(condition = sprintf("input['%s'] == 'tax'", "select_assay"),
actionButton("view_assay_tax",
"View",
class = "btn-primary"),
downloadButton('download_assay_tax', 'Download')
),
conditionalPanel(condition = sprintf("input['%s'] == 'annot'", "select_assay"),
actionButton("view_assay_annot",
"View",
class = "btn-primary"),
downloadButton('download_assay_annot', 'Download')
)
),
mainPanel(
conditionalPanel(condition = sprintf("input['%s'] == 'count'", "select_assay"),
DT::dataTableOutput("assay_table_count", width='95%')
),
conditionalPanel(condition = sprintf("input['%s'] == 'ra'", "select_assay"),
DT::dataTableOutput("assay_table_ra", width='95%')
),
conditionalPanel(condition = sprintf("input['%s'] == 'logcpm'", "select_assay"),
DT::dataTableOutput("assay_table_logcpm", width='95%')
),
conditionalPanel(condition = sprintf("input['%s'] == 'tax'", "select_assay"),
DT::dataTableOutput("assay_table_tax", width='95%')
),
conditionalPanel(condition = sprintf("input['%s'] == 'annot'", "select_assay"),
DT::dataTableOutput("assay_table_annot", width='95%')
)
)
)
)
)
)
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