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FreesearchR/inst/apps/data_analysis_modules/ui.R

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library(shiny)
library(bslib)
library(datamods)
library(shinyWidgets)
library(DT)
requireNamespace("gt")
# ns <- NS(id)
ui_elements <- list(
##############################################################################
#########
######### Import panel
#########
##############################################################################
"import" = bslib::nav_panel(
title = "Import",
shiny::fluidRow(
column(
width = 6,
shiny::h4("Choose your data source"),
shiny::conditionalPanel(
condition = "output.has_input=='yes'",
# Input: Select a file ----
shiny::helpText("Analyses are performed on provided data")
),
shiny::conditionalPanel(
condition = "output.has_input=='no'",
# Input: Select a file ----
shiny::radioButtons(
inputId = "source",
label = "Upload file or export from REDCap?",
selected = "file",
inline = TRUE,
choices = list(
"File" = "file",
"REDCap" = "redcap"
)
),
shiny::conditionalPanel(
condition = "input.source=='file'",
datamods::import_file_ui("file_import",
title = "Choose a datafile to upload",
file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta")
)
),
shiny::conditionalPanel(
condition = "input.source=='redcap'",
m_redcap_readUI("redcap_import")
)
)
),
column(
width = 6,
shiny::markdown("
# Welcome
This is the ***freesearchR*** web data analysis tool. An opiniotaed tool for easy data analysis at the hands of the clinician.
By intention, this is a focused app, with only few data modification tools included to keep the workflow streamlined.
")
)
),
shiny::conditionalPanel(
condition = "input.source=='redcap'",
DT::DTOutput(outputId = "redcap_prev")
),
shiny::br(),
shiny::actionButton(inputId = "act_start", label = "Start")
),
##############################################################################
#########
######### Data overview panel
#########
##############################################################################
"overview" = bslib::nav_panel(
title = "Overview and modifications",
bslib::navset_bar(fillable = TRUE,
# bslib::nav_panel(
# title = "Edit",
# datamods::edit_data_ui(id = "edit_data")
# ),
# bslib::nav_panel(
# title = "Overview",
# DT::DTOutput(outputId = "table")
# ),
bslib::nav_panel(
title = "Rename and select",
tags$h3("Select, rename and convert variables"),
fluidRow(
column(
width = 6,
# radioButtons()
shiny::actionButton("data_reset", "Restore original data"),
datamods::update_variables_ui("vars_update")
),
column(
width = 6,
tags$b("Original data:"),
# verbatimTextOutput("original"),
verbatimTextOutput("original_str"),
tags$b("Modified data:"),
# verbatimTextOutput("modified"),
verbatimTextOutput("modified_str")
)
)
),
bslib::nav_panel(
title = "Filter and modify",
shinyWidgets::html_dependency_winbox(),
fluidRow(
# column(
# width = 3,
# shiny::uiOutput("filter_vars"),
# shiny::conditionalPanel(
# condition = "(typeof input.filter_vars !== 'undefined' && input.filter_vars.length > 0)",
# datamods::filter_data_ui("filtering", max_height = "500px")
# )
# ),
# column(
# width = 9,
# DT::DTOutput(outputId = "filtered_table"),
# tags$b("Code dplyr:"),
# verbatimTextOutput(outputId = "filtered_code")
# ),
shiny::column(
width = 8,
toastui::datagridOutput2(outputId = "table_mod"),
shiny::tags$b("Reproducible code:"),
shiny::verbatimTextOutput(outputId = "filtered_code")
),
shiny::column(
width = 4,
shiny::actionButton("modal_cut", "Cut a variable"),
shiny::tags$br(),
shiny::tags$br(),
shiny::actionButton("modal_update", "Update factor's levels"),
shiny::tags$br(),
shiny::tags$br(),
IDEAFilter::IDEAFilter_ui("data_filter"),
shiny::actionButton("save_filter", "Apply the filter")
)
)
)
# column(
# 8,
# shiny::verbatimTextOutput("filtered_code"),
# DT::DTOutput("filtered_table")
# ),
# column(4, IDEAFilter::IDEAFilter_ui("data_filter"))
)
),
##############################################################################
#########
######### Data analyses panel
#########
##############################################################################
"analyze" = bslib::nav_panel(
title = "Analysis",
bslib::navset_bar(
title = "",
# bslib::layout_sidebar(
# fillable = TRUE,
sidebar = bslib::sidebar(
shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")),
shiny::uiOutput("outcome_var"),
shiny::uiOutput("strat_var"),
shiny::conditionalPanel(
condition = "input.strat_var!='none'",
shiny::radioButtons(
inputId = "add_p",
label = "Compare strata?",
selected = "no",
inline = TRUE,
choices = list(
"No" = "no",
"Yes" = "yes"
)
),
shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
),
shiny::radioButtons(
inputId = "all",
label = "Specify covariables",
inline = TRUE, selected = 2,
choiceNames = c(
"Yes",
"No"
),
choiceValues = c(1, 2)
),
shiny::conditionalPanel(
condition = "input.all==1",
shiny::uiOutput("include_vars")
),
shiny::radioButtons(
inputId = "specify_factors",
label = "Specify categorical variables?",
selected = "no",
inline = TRUE,
choices = list(
"Yes" = "yes",
"No" = "no"
)
),
shiny::conditionalPanel(
condition = "input.specify_factors=='yes'",
shiny::uiOutput("factor_vars")
),
bslib::input_task_button(
id = "load",
label = "Analyse",
icon = shiny::icon("pencil", lib = "glyphicon"),
label_busy = "Working...",
icon_busy = fontawesome::fa_i("arrows-rotate",
class = "fa-spin",
"aria-hidden" = "true"
),
type = "primary",
auto_reset = TRUE
),
shiny::helpText("If you change the parameters, press 'Analyse' again to update the tables")
# )
),
bslib::nav_panel(
title = "Baseline characteristics",
gt::gt_output(outputId = "table1")
),
bslib::nav_panel(
title = "Regression table",
gt::gt_output(outputId = "table2")
),
bslib::nav_panel(
title = "Regression checks",
shiny::plotOutput(outputId = "check")
)
)
),
##############################################################################
#########
######### Documentation panel
#########
##############################################################################
"docs" = bslib::nav_panel(
title = "Documentation",
shiny::markdown(readLines("www/intro.md")),
shiny::br()
)
)
# cards <- list(
# "overview"=bslib::card(
# title = "Data overview",
# # shiny::uiOutput("data.classes"),
# # shiny::uiOutput("data.input"),
# # shiny::p("Classes of uploaded data"),
# # gt::gt_output("data.classes"),
# shiny::p("Subset data"),
# DT::DTOutput(outputId = "data_table")
# ),
# "baseline"=bslib::card(
# title = "Baseline characteristics",
# gt::gt_output(outputId = "table1")
# ),
# "regression"= bslib::card(
# title = "Regression table",
# gt::gt_output(outputId = "table2")
# ),
# "checks" =bslib::card(
# title = "Regression checks",
# shiny::plotOutput(outputId = "check")
# )
# )
ui <- bslib::page(
title = "freesearcheR",
theme = bslib::bs_theme(
primary = "#1E4A8F",
secondary = "#FF6F61",
bootswatch = "minty",
base_font = bslib::font_google("Montserrat"),
code_font = bslib::font_google("Open Sans")
),
bslib::page_navbar(
id = "main_panel",
ui_elements$import,
ui_elements$overview,
ui_elements$analyze,
ui_elements$docs
)
)
# ui <- bslib::page(
# theme = bslib::bs_theme(
# bootswatch = "minty",
# base_font = font_google("Inter"),
# code_font = font_google("JetBrains Mono")
# ),
# title = "fresearcheR - free, web-based research analyses",
# bslib::page_navbar(
# title = "fresearcheR - free, web-based research analyses",
# header = h6("Welcome to the fresearcheR tool. This is an early alpha version to act as a proof-of-concept and in no way intended for wider public use."),
# sidebar = bslib::sidebar(
# width = 300,
# open = "open",
# shiny::h4("Upload your dataset"),
# shiny::conditionalPanel(
# condition = "output.has_input=='yes'",
# # Input: Select a file ----
# shiny::helpText("Analyses are performed on provided data")
# ),
# shiny::conditionalPanel(
# condition = "output.has_input=='no'",
# # Input: Select a file ----
# shiny::radioButtons(
# inputId = "source",
# label = "Upload file or export from REDCap?",
# selected = "file",
# inline = TRUE,
# choices = list(
# "File" = "file",
# "REDCap" = "redcap"
# )
# ),
# shiny::conditionalPanel(
# condition = "input.source=='file'",
# datamods::import_file_ui("file_import",
# file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav",".ods",".dta"))
# )
# ,
# shiny::conditionalPanel(
# condition = "input.source=='redcap'",
# m_redcap_readUI("redcap_import")
# ),
# # Does not work??
# # shiny::actionButton(inputId = "test_data",
# # label = "Load test data", class = "btn-primary")
# ),
# shiny::conditionalPanel(
# condition = "output.uploaded=='yes'",
# shiny::h4("Parameter specifications"),
# shiny::radioButtons(
# inputId = "factorize",
# label = "Factorize variables with few levels?",
# selected = "yes",
# inline = TRUE,
# choices = list(
# "Yes" = "yes",
# "No" = "no"
# )
# ),
# shiny::radioButtons(
# inputId = "regression_auto",
# label = "Automatically choose function",
# inline = TRUE,
# choiceNames = c(
# "Yes",
# "No"
# ),
# choiceValues = c(1, 2)
# ),
# shiny::conditionalPanel(
# condition = "input.regression_auto==2",
# shiny::textInput(
# inputId = "regression_formula",
# label = "Formula string to render with 'glue::glue'",
# value = NULL
# ),
# shiny::textInput(
# inputId = "regression_fun",
# label = "Function to use for analysis (needs pasckage and name)",
# value = "stats::lm"
# ),
# shiny::textInput(
# inputId = "regression_args",
# label = "Arguments to pass to the function (provided as a string)",
# value = ""
# )
# ),
# shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")),
# shiny::uiOutput("outcome_var"),
# shiny::uiOutput("strat_var"),
# shiny::conditionalPanel(
# condition = "input.strat_var!='none'",
# shiny::radioButtons(
# inputId = "add_p",
# label = "Compare strata?",
# selected = "no",
# inline = TRUE,
# choices = list(
# "No" = "no",
# "Yes" = "yes"
# )
# ),
# shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
# ),
# shiny::radioButtons(
# inputId = "all",
# label = "Specify covariables",
# inline = TRUE, selected = 2,
# choiceNames = c(
# "Yes",
# "No"
# ),
# choiceValues = c(1, 2)
# ),
# shiny::conditionalPanel(
# condition = "input.all==1",
# shiny::uiOutput("include_vars")
# ),
# shiny::radioButtons(
# inputId = "specify_factors",
# label = "Specify categorical variables?",
# selected = "no",
# inline = TRUE,
# choices = list(
# "Yes" = "yes",
# "No" = "no"
# )
# ),
# shiny::conditionalPanel(
# condition = "input.specify_factors=='yes'",
# shiny::uiOutput("factor_vars")
# ),
# bslib::input_task_button(
# id = "load",
# label = "Analyse",
# icon = shiny::icon("pencil", lib = "glyphicon"),
# label_busy = "Working...",
# icon_busy = fontawesome::fa_i("arrows-rotate",
# class = "fa-spin",
# "aria-hidden" = "true"
# ),
# type = "primary",
# auto_reset = TRUE
# ),
# shiny::helpText("If you change the parameters, press 'Analyse' again to update the tables"),
# # shiny::actionButton("load", "Analyse", class = "btn-primary"),
# #
# # # Horizontal line ----
# tags$hr(),
# shiny::conditionalPanel(
# condition = "input.load",
# h4("Download results"),
# shiny::helpText("Choose your favourite output file format for further work."),
# shiny::selectInput(
# inputId = "output_type",
# label = "Choose your desired output format",
# selected = NULL,
# choices = list(
# "Word" = "docx",
# "LibreOffice" = "odt"
# # ,
# # "PDF" = "pdf",
# # "All the above" = "all"
# )
# ),
#
# # Button
# downloadButton(
# outputId = "report",
# label = "Download",
# icon = shiny::icon("download")
# )
# )
# )
# ),
# bslib::nav_spacer(),
# panels[[1]],
# panels[[2]],
# panels[[3]],
# panels[[4]]
#
# # layout_columns(
# # cards[[1]]
# # ),
# # layout_columns(
# # cards[[2]], cards[[3]]
# # )
# )
# )
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