#' Statmodel UI module for statistical inference UI.
#'
#' This function sets up the Statmodel UI where it consists of several,
#' options for users to select and upload files.
#'
#' @param id namespace prefix for the module
#'
#' @return This function returns nothing, as it sets up the Statmodel UI
#'
statmodelUI <- function(id) {
ns <- NS(id)
tagList(
fluidPage(
tags$head(
tags$style(HTML('#statmodel-submit3{background-color:orange}')),
tags$style(HTML('#statmodel-clear3{background-color:orange}')),
tags$style(HTML('#statmodel-submit1{background-color:orange}')),
tags$style(HTML('#statmodel-clear1{background-color:orange}')),
tags$style(HTML('#statmodel-submit2{background-color:orange}')),
tags$style(HTML('#statmodel-clear2{background-color:orange}')),
tags$style(HTML('#statmodel-calculate{background-color:orange}')),
tags$style(HTML('#statmodel-plotresults{background-color:orange}')),
tags$style(HTML('#statmodel-viewresults{background-color:orange}')),
tags$style(HTML('#statmodel-submit{background-color:orange}')),
tags$style(HTML('#statmodel-clear{background-color:orange}')),
tags$link(rel = "stylesheet", type = "text/css", href = "assets/style.css"),
),
use_busy_spinner(spin = "fading-circle"),
headerPanel("Statistical modeling and inference"),
p("In this tab a statistical model is built in three steps:"),
p("(i) Create a contrast matrix with the correct Group comparisons,"),
p("(ii) generate the model and "),
p("(iii) view result plots."),
p("More info ", a("here", href="https://www.rdocumentation.org/packages/MSstats/versions/3.4.0/topics/groupComparisonPlots")),
# statistical model
sidebarPanel(
fluidRow(
radioButtons(ns("def_comp"), label=h4("1. Define comparisons\
- contrast matrix",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
div("Define what conditions you want to compare here.", class = "icon-tooltip")),
c("All possible pairwise comparisons" = "all_pair",
"Compare all against one" = "all_one",
"Create custom pairwise comparisons" = "custom",
"Create custom non-pairwise comparisons" = "custom_np"),
selected = character(0)),
tags$br(),
conditionalPanel(condition = "input['statmodel-def_comp'] == 'custom'",
uiOutput(ns('choice1')),
h6("vs"),
uiOutput(ns("choice2")),
actionButton(ns("submit"), "Add"),
actionButton(ns("clear"), "Clear matrix")
),
conditionalPanel(condition = "input['statmodel-def_comp'] == 'all_one'",
h5("Compare all groups against:"),
uiOutput(ns("choice3")),
actionButton(ns("submit1"), "Submit"),
actionButton(ns("clear1"), "Clear matrix")
),
conditionalPanel(condition = "input['statmodel-def_comp'] == 'all_pair'",
actionButton(ns("submit2"), "Submit"),
actionButton(ns("clear2"), "Clear matrix")
),
conditionalPanel(condition = "input['statmodel-def_comp'] == 'custom_np'",
h5("Non-pairwise Comparison:"),
uiOutput(ns('comp_name')),
uiOutput(ns('weights')),
actionButton(ns("submit3"), "Add"),
actionButton(ns("clear3"), "Clear matrix")
),
tags$hr(),
h4("2. Group comparison"),
p("Please add a comparison matrix before modeling."),
disabled(actionButton(ns("calculate"), "Start")),
tags$hr(),
conditionalPanel(condition = "input['loadpage-DDA_DIA'] == 'TMT' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT')",
radioButtons(ns("moderated"),
label= h4("Empirical Bayes moderation",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
div("TRUE will moderate t statistic; FALSE (default) uses ordinary t statistic.", class = "icon-tooltip")),
c(True = TRUE, False = FALSE))),
sliderInput(ns("signif"),
label = h5("Significance level",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
div("The alpha used to determine significant results. IE the probability of type I error)", class = "icon-tooltip")),
0, 1, 0.05),
),
# table of significant proteins
tags$br(),
fluidRow(
column(12,
fluidRow(
selectInput(ns("typeplot"),
label = h4("3. Visualization - \
select plot type"),
c("Volcano Plot" = "VolcanoPlot",
"Heatmap"="Heatmap",
"Comparison Plot"="ComparisonPlot"))), #
conditionalPanel(condition = "input['statmodel-typeplot'] == 'VolcanoPlot'",
uiOutput(ns("WhichComp")),
conditionalPanel(
condition = "input['loadpage-DDA_DIA']!=='TMT'",
checkboxInput(ns("pname"), label = p("display protein name"))),
selectInput(ns("logp"),
label = h5("Log transformation of adjusted p-value"),
c("base 2" = "2", "base 10" = "10"), selected = "10"),
sliderInput(ns("sig"),
label = h5("Adjusted p-value cutoff",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
div("The cutoff used to determine significant results.)", class = "icon-tooltip")),
0, 1, 0.05),
checkboxInput(ns("FC1"),
label = p("Apply specific fold change cutoff for significance")),
conditionalPanel(
condition = "input['statmodel-FC1'] == true",
numericInput(ns("FC"), "Fold change cutoff",
1, 0, 100,
0.1)),
tags$br()),
conditionalPanel(
condition = "input['statmodel-typeplot'] == 'ComparisonPlot'",
uiOutput(ns("WhichProt")),
uiOutput(ns("WhichComp1"))),
conditionalPanel(
condition = "input['statmodel-typeplot'] == 'Heatmap'",
h4("Note: Only one page will be shown in \
browser. To view all proteins please \
view this plot as a pdf. \
Heatmaps require at least two comparisons."),
selectInput(ns("logp"),
label = h5("Log transformation of adjusted p-value"),
c("base 2" = "2", "base 10" = "10"), selected = "10"),
checkboxInput(ns("FC1"),
label = p("Apply specific fold change cutoff for significance")),
conditionalPanel(
condition = "input['statmodel-FC1'] == true",
numericInput(ns("FC"), "cutoff",
1, 0, 100,
0.1)),
numericInput(ns("nump"), "Number of proteins \
per page", 100, 1, 180, 1),
selectInput(ns("cluster"),
label = h5("Cluster analysis",class = "icon-wrapper",icon("question-circle", lib = "font-awesome"),
div("Determines how to order proteins and comparisons. protein means, comparison means, or both", class = "icon-tooltip")),
c("protein dendogram" = "protein",
"comparison dendogram" = "comparison",
"protein and comparison dendograms" = "both"))),
p("Please note if you want to plot more than one \
Volcano Plot comparison, you must save the results \
as a pdf."),
conditionalPanel(
condition = "input['loadpage-BIO'] !== 'PTM'",
actionButton(ns("viewresults"),
"View plot in browser (only for one \
comparison/protein)")),
downloadButton(ns("plotresults"), "Save plot results as pdf")
)
)
),
fluidRow(
column(7,
fluidRow(uiOutput(ns('code.button')),
column(7,offset = 10,
disabled(actionButton(inputId = ns("Design"), label = "Next Step")),
tags$br(),
tags$br(),
)),
uiOutput(ns("matrix")),
conditionalPanel(condition = "input['loadpage-BIO']=='PTM'",
tabsetPanel(
tabPanel("Adjusted PTM Results",
uiOutput(ns("adj_table_results"))),
tabPanel("Unadjusted PTM Results",
uiOutput(ns("unadj_table_results"))),
tabPanel("Protein Results",
uiOutput(ns("prot_table_results")))
)
),
conditionalPanel(condition = "input['loadpage-BIO']!=='PTM'",
uiOutput(ns("table_results"))
),
tags$br(),
uiOutput(ns("comparison_plots"))
))
)
)
}
