/
ui.R
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ui.R
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#
# This is the user-interface definition of the web application.
#
suppressPackageStartupMessages(library(shinyWidgets))
suppressPackageStartupMessages(library(shinycssloaders))
options(spinner.type=5)
appLoadCSS <- "
#loading-content {
position: absolute;
background: #000000;
opacity: 0.9;
z-index: 100;
left: 0;
right: 0;
height: 100%;
text-align: center;
color: #FFFFFF;
}
"
tabControlJS <- "
shinyjs.disableTab = function(name) {
var tab = $('.nav li a[data-value=' + name + ']');
tab.bind('click.tab', function(e) {
e.preventDefault();
return false;
});
tab.addClass('disabled');
}
shinyjs.enableTab = function(name) {
var tab = $('.nav li a[data-value=' + name + ']');
tab.unbind('click.tab');
tab.removeClass('disabled');
}
"
tabControlCSS <- "
.nav li a.disabled {
background-color: unset !important;
color: grey !important;
cursor: not-allowed !important;
}"
wellpanel.settings.style = "background: white; margin-top: 15px; margin-bottom: 0px; padding-top: 3px; padding-bottom: 3px;"
# Define UI for application that draws a histogram
shinyUI(fluidPage(title = "SCAN-B MutationExplorer",
useShinyjs(),
extendShinyjs(text = tabControlJS, functions = c("enableTab", "disableTab")),
inlineCSS(c(tabControlCSS, appLoadCSS)),
# Enable Google Analytics
tags$head(includeScript("google-analytics.js")),
# Style validation errors, and fields with invalid values.
tags$head(tags$style(HTML("
.shiny-output-error-validation {
color: red;
font-size: 150%;
}
input:invalid {
background-color: #FFCCCC;
}"))
),
# Loading message
div(id = "loading-content",
h2("Loading...")
),
hidden(
div(id = "app-content",
titlePanel(h1(config$app_title,
h3(paste(prettyNum(n.mut, big.mark=","),
"mutations in",
prettyNum(n.samples, big.mark=","),
"Primary Breast Cancer Transcriptomes")))
),
sidebarLayout(
sidebarPanel(
tabsetPanel(type = "pills",
tabPanel("Plot and Data Selection",
wellPanel(style = wellpanel.settings.style,
h4("Plot Selection"),
helper(selectInput("plotType", "Plot Type", plot.type.options),
content = "plot_type"),
conditionalPanel(
condition = "input.plotType == 'mut.gene.plot'",
helper(selectizeInput("gene.input",
sprintf("Genes (1-%d)", survival.gene.plots.max),
choices = names(mutated.gene.columns), multiple = TRUE,
options = list(maxItems = survival.gene.plots.max,
plugins = list('remove_button'))), # enable deselection of items
content = "gene_selection")
),
# pathway plot specific settings
conditionalPanel(
condition = "input.plotType == 'mut.pathway.plot'",
# choice between existing and custom pathway
helper(selectInput("pathwayType", "Pathway Definition Source", pathway.type.options),
content = "pathway_definition_source"),
conditionalPanel(
condition = "input.pathwayType == 'pathway.reactome'",
selectizeInput("pathway.input",
sprintf("Reactome Pathways (1-%d)", survival.pathway.plots.max),
choices = pathway.ui.options,
multiple = TRUE,
options = list(maxItems = survival.gene.plots.max,
plugins = list('remove_button'))) # enable deselection of items
),
conditionalPanel(
condition = "input.pathwayType == 'pathway.custom'",
selectizeInput("custom.pathway.input",
sprintf("Genes in Custom Pathway (1-%d)", pathway.custom.genes.max),
choices = names(mutated.gene.columns),
multiple = TRUE,
options = list(maxItems = pathway.custom.genes.max,
plugins = list('remove_button'))) # enable deselection of items
)
),
# burden plot specific settings
conditionalPanel(
condition = "input.plotType == 'mut.burden.plot'",
helper(radioGroupButtons("tmb.type",
label = "Burden Type", choices = tmb.type.options, selected = tmb.type.options[1],
status = "primary", individual = TRUE),
content = "tmb_type"),
helper(sliderInput("tmb.cutoff", "Burden Cutoff", min = 1, max = 10, value = 5, step = 1),
content = "tmb_cutoff")
),
# waterfall plot specific settings
conditionalPanel(
condition = "input.plotType == 'mut.waterfall.plot'",
helper(numericInput("waterfall.cutoff",
sprintf("Number of most mutated genes (%d-%d)", plot.waterfall.cutoff.min, plot.waterfall.cutoff.max),
min = plot.waterfall.cutoff.min,
max = plot.waterfall.cutoff.max,
value = plot.waterfall.cutoff.default),
content = "waterfall_cutoff")
),
# protein plot specific settings
conditionalPanel(
condition = "input.plotType == 'mut.protein.plot'",
selectizeInput("protein.plot.gene", "Gene",
choices = names(mutated.gene.columns),
selected = names(mutated.gene.columns)[2], # updated on the server side
multiple=FALSE)
)
),
wellPanel(style = wellpanel.settings.style,
helper(h4("Mutation Selection"),
content = "mutation_selection"),
radioGroupButtons("mutationSelection",
label = "", choices = mutation.selection.options, selected = "mutations.all",
status = "primary", individual = TRUE),
pickerInput(inputId = "mutationEffect",
label = "Mutation Effect",
choices = mut.effect.tbl$effect,
choicesOpt = list(content = mut.effect.html.labels),
selected = mut.effect.tbl$effect,
options = list(
`actions-box` = TRUE
),
multiple = TRUE
)
),
wellPanel(style = wellpanel.settings.style,
helper(h4("Sample Selection"),
content = "sample_selection"),
selectInput("treatment.input", "Treatment Group",
choices = treatment.options),
radioGroupButtons("hist.type",
label = "Histological Type", choices = ui.options$HistType, selected = ui.options$HistType[["Any"]],
status = "primary", individual = TRUE),
radioGroupButtons("hr.cutoff",
label = "ER/PgR Cutoff", choices = hr.cutoff.options, selected = hr.cutoff.options[1],
status = "primary", individual = TRUE),
radioGroupButtons("er.status",
label = "ER Status", choices = ui.options$ER, selected = ui.options$ER[["Any"]],
status = "primary", individual = TRUE),
radioGroupButtons("pgr.status",
label = "PgR Status", choices = ui.options$PgR, selected = ui.options$PgR[["Any"]],
status = "primary", individual = TRUE),
radioGroupButtons("her2.status",
label = "HER2 Status", choices = ui.options$HER2, selected = ui.options$HER2[["Any"]],
status = "primary", individual = TRUE),
radioGroupButtons("ki67.status",
label = "Ki67 Status", choices = ui.options$Ki67, selected = ui.options$Ki67[["Any"]],
status = "primary", individual = TRUE),
radioGroupButtons("nhg",
label = "NHG", choices = ui.options$NHG, selected = ui.options$NHG[["Any"]],
status = "primary", individual = TRUE),
pickerInput(inputId = "pam50",
label = "PAM50 Subtype",
choices = ui.options$PAM50, choicesOpt = list(content = pam50.html.labels))
)
),
tabPanel("Plot Settings",
conditionalPanel(
condition = "input.plotType == 'mut.gene.plot' ||
input.plotType == 'mut.pathway.plot' ||
input.plotType == 'mut.burden.plot'",
wellPanel(style = wellpanel.settings.style,
helper(h4("Plot Dimensions"),
content = "plot_dimensions"),
splitLayout(
numericInput("height.survival",
label = sprintf("Height (%d-%d)", plot.survival.height.min, plot.survival.height.max),
min = plot.survival.height.min,
max = plot.survival.height.max,
value = plot.survival.height.default
),
numericInput("width.survival",
label = sprintf("Width (%d-%d)", plot.survival.width.min, plot.survival.width.max),
min = plot.survival.width.min,
max = plot.survival.width.max,
value = plot.survival.width.default
)
)
),
wellPanel(style = wellpanel.settings.style,
helper(h4("Color Settings"),
content = "color_settings"),
selectInput("color.palette", "Color Palette",
choices = color.palette.options, selected = color.palette.options[["JCO"]],
multiple = FALSE)
),
wellPanel(style = wellpanel.settings.style,
helper(h4("Legend Settings"),
content = "legend_settings"),
awesomeCheckbox("showLegend",
label = "Show Legend",
value = TRUE),
conditionalPanel(
condition = "input.showLegend == true",
textInput("legendTitle", "Legend Title", value = "strata"),
selectInput("legendLoc", "Legend Location",
choices = plot.legend.loc.options),
conditionalPanel(
condition = "input.legendLoc == 'custom'",
splitLayout(
sliderInput("legend.coord.x", "X Coordinate", min = 0, max = 1,
value = 0.25, step = 0.01),
sliderInput("legend.coord.y", "Y Coordinate", min = 0, max = 1,
value = 0.25, step = 0.01)
)
)
)
),
wellPanel(style = wellpanel.settings.style,
helper(h4("Plot Features"),
content = "plot_features"),
awesomeCheckbox("show.risk.table",
label = "Show risk table",
value = TRUE),
awesomeCheckbox("show.pval",
label = "Show logrank p-value",
value = TRUE),
awesomeCheckbox("show.censors",
label = "Show censors",
value = FALSE),
awesomeCheckbox("show.conf.int",
label = "Show confidence intervals",
value = FALSE)
)
),
conditionalPanel(
condition = "input.plotType == 'mut.waterfall.plot'",
wellPanel(style = wellpanel.settings.style,
helper(h4("Plot Dimensions"),
content = "plot_dimensions"),
splitLayout(
numericInput("height.waterfall",
label = sprintf("Height (%d-%d)", plot.waterfall.height.min, plot.waterfall.height.max),
min = plot.waterfall.height.min,
max = plot.waterfall.height.max,
value = plot.waterfall.height.default
),
numericInput("width.waterfall",
label = sprintf("Width (%d-%d)", plot.waterfall.width.min, plot.waterfall.width.max),
min = plot.waterfall.width.min,
max = plot.waterfall.width.max,
value = plot.waterfall.width.default
)
)
),
wellPanel(style = wellpanel.settings.style,
helper(h4("General Settings"),
content = "plot_settings_waterfall"),
numericInput("waterfall.round.digits",
label = sprintf("Frequency Digits (%d-%d)", plot.waterfall.round.digits.min, plot.waterfall.round.digits.max),
min = plot.waterfall.round.digits.min,
max = plot.waterfall.round.digits.max,
value = plot.waterfall.round.digits.default
),
awesomeCheckbox("includeWildtypeSamples",
label = "Include Wildtype Samples",
value = TRUE)
)
),
conditionalPanel(
condition = "input.plotType == 'mut.protein.plot'",
wellPanel(style = wellpanel.settings.style,
helper(h4("Plot Dimensions"),
content = "plot_dimensions"),
splitLayout(
numericInput("height.protein",
label = sprintf("Height (%d-%d)", plot.protein.height.min, plot.protein.height.max),
min = plot.protein.height.min,
max = plot.protein.height.max,
value = plot.protein.height.default
),
numericInput("width.protein",
label = sprintf("Width (%d-%d)", plot.protein.width.min, plot.protein.width.max),
min = plot.protein.width.min,
max = plot.protein.width.max,
value = plot.protein.width.default
)
)
),
wellPanel(style = wellpanel.settings.style,
helper(h4("Plot Settings"),
content = "protein_plot_settings"),
numericInput("protein.plot.mutation.cutoff",
label = "Mutation Cutoff",
min = plot.protein.cutoff.mutation.min,
value = plot.protein.cutoff.mutation.default
),
numericInput("protein.plot.anno.cutoff",
label = "Annotation Cutoff",
min = plot.protein.cutoff.mutation.min,
value = plot.protein.cutoff.annotation.default
)
)
)
)
),
wellPanel(style = wellpanel.settings.style,
helper(h3("Downloads"),
content = "downloads"),
splitLayout(
downloadButton("downloadPlot", label = "Plot PDF"),
downloadButton("downloadSamples", label = "Sample TSV"),
downloadButton("downloadMutations", label = "Mutation TSV")
),
HTML("<br>") # for vertical space below the buttons
)
),
# Plots, data tables, and statistics
mainPanel(
tabsetPanel(type = "pills",
tabPanel("Plots", value = "plotTab", style = "padding-top:30px",
withSpinner(plotOutput("plot"))
),
tabPanel("Sample Table", value = "sampleTab",
DT::dataTableOutput("sample.table")
),
tabPanel("Mutation Table", value = "mutationTab",
DT::dataTableOutput("mut.table")
),
tabPanel("Dataset Statistics", value = "statsTab",
htmlOutput("datasetStats")
),
tabPanel("Citation and About", value = "aboutTab",
htmlOutput("appCiteAbout"),
h2("Session Information"),
verbatimTextOutput("sessionInfo")
)
)
)
)
))
))