mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 01:49:39 +02:00
new ui
This commit is contained in:
parent
c7b879f458
commit
ec5603d368
4 changed files with 807 additions and 745 deletions
164
R/data_plots.R
164
R/data_plots.R
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@ -11,97 +11,96 @@
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data_visuals_ui <- function(id, tab_title = "Plots", ...) {
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ns <- shiny::NS(id)
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# bslib::navset_bar(
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list(
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# Sidebar with a slider input
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sidebar = bslib::sidebar(
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bslib::accordion(
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multiple = FALSE,
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bslib::accordion_panel(
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title = "Creating plot",
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icon = bsicons::bs_icon("graph-up"),
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shiny::uiOutput(outputId = ns("primary")),
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shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
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shiny::tags$br(),
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shiny::uiOutput(outputId = ns("type")),
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shiny::uiOutput(outputId = ns("secondary")),
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shiny::uiOutput(outputId = ns("tertiary")),
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shiny::br(),
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shiny::actionButton(
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inputId = ns("act_plot"),
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label = "Plot",
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width = "100%",
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icon = shiny::icon("palette"),
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disabled = FALSE
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bslib::layout_sidebar(
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sidebar = bslib::sidebar(
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bslib::accordion(
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multiple = FALSE,
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bslib::accordion_panel(
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title = "Creating plot",
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icon = bsicons::bs_icon("graph-up"),
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shiny::uiOutput(outputId = ns("primary")),
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shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
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shiny::tags$br(),
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shiny::uiOutput(outputId = ns("type")),
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shiny::uiOutput(outputId = ns("secondary")),
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shiny::uiOutput(outputId = ns("tertiary")),
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shiny::br(),
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shiny::actionButton(
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inputId = ns("act_plot"),
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label = "Plot",
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width = "100%",
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icon = shiny::icon("palette"),
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disabled = FALSE
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),
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shiny::helpText('Adjust settings, then press "Plot".')
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),
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shiny::helpText('Adjust settings, then press "Plot".')
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),
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# bslib::accordion_panel(
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# title = "Advanced",
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# icon = bsicons::bs_icon("gear")
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# ),
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bslib::accordion_panel(
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title = "Download",
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icon = bsicons::bs_icon("download"),
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shinyWidgets::noUiSliderInput(
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inputId = ns("height_slide"),
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label = "Plot height (mm)",
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min = 50,
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max = 300,
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value = 100,
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step = 1,
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format = shinyWidgets::wNumbFormat(decimals = 0),
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color = datamods:::get_primary_color(),
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inline = TRUE
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),
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# shiny::numericInput(
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# inputId = ns("height_numeric"),
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# label = "Plot height (mm)",
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# min = 50,
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# max = 300,
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# value = 100
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# ),
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shinyWidgets::noUiSliderInput(
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inputId = ns("width"),
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label = "Plot width (mm)",
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min = 50,
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max = 300,
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value = 100,
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step = 1,
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format = shinyWidgets::wNumbFormat(decimals = 0),
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color = datamods:::get_primary_color()
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),
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shiny::selectInput(
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inputId = ns("plot_type"),
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label = "File format",
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choices = list(
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"png",
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"tiff",
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"eps",
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"pdf",
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"jpeg",
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"svg"
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bslib::accordion_panel(
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title = "Download",
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icon = bsicons::bs_icon("download"),
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shinyWidgets::noUiSliderInput(
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inputId = ns("height_slide"),
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label = "Plot height (mm)",
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min = 50,
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max = 300,
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value = 100,
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step = 1,
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format = shinyWidgets::wNumbFormat(decimals = 0),
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color = datamods:::get_primary_color(),
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inline = TRUE
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),
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# shiny::numericInput(
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# inputId = ns("height_numeric"),
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# label = "Plot height (mm)",
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# min = 50,
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# max = 300,
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# value = 100
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# ),
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shinyWidgets::noUiSliderInput(
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inputId = ns("width"),
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label = "Plot width (mm)",
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min = 50,
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max = 300,
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value = 100,
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step = 1,
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format = shinyWidgets::wNumbFormat(decimals = 0),
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color = datamods:::get_primary_color()
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),
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shiny::selectInput(
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inputId = ns("plot_type"),
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label = "File format",
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choices = list(
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"png",
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"tiff",
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"eps",
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"pdf",
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"jpeg",
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"svg"
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)
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),
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shiny::br(),
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# Button
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shiny::downloadButton(
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outputId = ns("download_plot"),
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label = "Download plot",
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icon = shiny::icon("download")
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)
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),
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shiny::br(),
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# Button
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shiny::downloadButton(
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outputId = ns("download_plot"),
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label = "Download plot",
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icon = shiny::icon("download")
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)
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)
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)
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),
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bslib::nav_panel(
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title = tab_title,
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),
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shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a(
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href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
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"View notes in new tab",
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target = "_blank",
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rel = "noopener noreferrer"
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))
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),
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shiny::plotOutput(ns("plot"), height = "70vh"),
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shiny::tags$br(),
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shiny::tags$br(),
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shiny::htmlOutput(outputId = ns("code_plot"))
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)
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)
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# )
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}
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@ -725,6 +724,7 @@ get_label <- function(data, var = NULL) {
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#' paste(sample(letters[1:10], 100, TRUE), collapse = "") |> line_break(force = TRUE)
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line_break <- function(data, lineLength = 20, force = FALSE) {
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if (isTRUE(force)) {
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## This eats some letters when splitting a sentence... ??
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gsub(paste0("(.{1,", lineLength, "})(\\s|[[:alnum:]])"), "\\1\n", data)
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} else {
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paste(strwrap(data, lineLength), collapse = "\n")
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@ -746,7 +746,7 @@ line_break <- function(data, lineLength = 20, force = FALSE) {
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wrap_plot_list <- function(data,
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tag_levels = NULL,
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title = NULL,
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axis.font.family=NULL,
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axis.font.family = NULL,
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...) {
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if (ggplot2::is_ggplot(data[[1]])) {
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if (length(data) > 1) {
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@ -44,14 +44,7 @@ data_missings_server <- function(id,
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tryCatch(
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{
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if (!is.null(by_var) && by_var != "" && by_var %in% names(df_tbl)) {
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df_tbl[[by_var]] <- ifelse(is.na(df_tbl[[by_var]]), "Missing", "Non-missing")
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out <- gtsummary::tbl_summary(df_tbl, by = by_var) |>
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gtsummary::add_p()
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} else {
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out <- gtsummary::tbl_summary(df_tbl)
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}
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out <- compare_missings(df_tbl,by_var)
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},
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error = function(err) {
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showNotification(paste0("Error: ", err), type = "err")
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@ -129,10 +122,22 @@ missing_demo_app <- function() {
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missing_demo_app()
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#' Pairwise comparison of missings across covariables
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#'
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#' @param data data frame
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#' @param by_var variable to stratify by missingness
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#'
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#' @returns gtsummary list object
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#' @export
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#'
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compare_missings <- function(data,by_var){
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if (!is.null(by_var) && by_var != "" && by_var %in% names(data)) {
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data[[by_var]] <- ifelse(is.na(data[[by_var]]), "Missing", "Non-missing")
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out <- gtsummary::tbl_summary(data, by = by_var) |>
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gtsummary::add_p()
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} else {
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out <- gtsummary::tbl_summary(data)
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}
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out
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}
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@ -44,155 +44,173 @@ regression_ui <- function(id, ...) {
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ns <- shiny::NS(id)
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shiny::tagList(
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title = "",
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sidebar = bslib::sidebar(
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shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
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bslib::accordion(
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open = "acc_reg",
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multiple = FALSE,
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bslib::accordion_panel(
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value = "acc_reg",
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title = "Regression",
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icon = bsicons::bs_icon("calculator"),
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shiny::uiOutput(outputId = ns("outcome_var")),
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# shiny::selectInput(
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# inputId = "design",
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# label = "Study design",
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# selected = "no",
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# inline = TRUE,
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# choices = list(
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# "Cross-sectional" = "cross-sectional"
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# )
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# ),
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shiny::uiOutput(outputId = ns("regression_type")),
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shiny::radioButtons(
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inputId = ns("all"),
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label = "Specify covariables",
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inline = TRUE, selected = 2,
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choiceNames = c(
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"Yes",
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"No"
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),
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choiceValues = c(1, 2)
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),
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shiny::conditionalPanel(
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condition = "input.all==1",
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shiny::uiOutput(outputId = ns("regression_vars")),
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shiny::helpText("If none are selected, all are included."),
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shiny::tags$br(),
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ns = ns
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),
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bslib::input_task_button(
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id = ns("load"),
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label = "Analyse",
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icon = bsicons::bs_icon("pencil"),
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label_busy = "Working...",
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icon_busy = fontawesome::fa_i("arrows-rotate",
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class = "fa-spin",
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"aria-hidden" = "true"
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),
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type = "secondary",
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auto_reset = TRUE
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),
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shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
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shiny::tags$br(),
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shiny::radioButtons(
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inputId = ns("add_regression_p"),
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label = "Show p-value",
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inline = TRUE,
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selected = "yes",
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choices = list(
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"Yes" = "yes",
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"No" = "no"
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)
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),
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# shiny::tags$br(),
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# shiny::radioButtons(
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# inputId = ns("tbl_theme"),
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# label = "Show p-value",
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# inline = TRUE,
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# selected = "jama",
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# choices = list(
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# "JAMA" = "jama",
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# "Lancet" = "lancet",
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# "NEJM" = "nejm"
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# )
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# ),
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shiny::tags$br()
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),
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do.call(
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bslib::accordion_panel,
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c(
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list(
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value = "acc_plot",
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title = "Coefficient plot",
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icon = bsicons::bs_icon("bar-chart-steps"),
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# title = "",
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bslib::nav_panel(
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title = "Regression table",
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bslib::layout_sidebar(
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sidebar = bslib::sidebar(
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shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
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bslib::accordion(
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open = "acc_reg",
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multiple = FALSE,
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bslib::accordion_panel(
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value = "acc_reg",
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title = "Regression",
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icon = bsicons::bs_icon("calculator"),
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shiny::uiOutput(outputId = ns("outcome_var")),
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# shiny::selectInput(
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# inputId = "design",
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# label = "Study design",
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# selected = "no",
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# inline = TRUE,
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# choices = list(
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# "Cross-sectional" = "cross-sectional"
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# )
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# ),
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shiny::uiOutput(outputId = ns("regression_type")),
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shiny::radioButtons(
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inputId = ns("all"),
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label = "Specify covariables",
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inline = TRUE, selected = 2,
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choiceNames = c(
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"Yes",
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"No"
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),
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choiceValues = c(1, 2)
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),
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shiny::conditionalPanel(
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condition = "input.all==1",
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shiny::uiOutput(outputId = ns("regression_vars")),
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shiny::helpText("If none are selected, all are included."),
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shiny::tags$br(),
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ns = ns
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),
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bslib::input_task_button(
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id = ns("load"),
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label = "Analyse",
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icon = bsicons::bs_icon("pencil"),
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label_busy = "Working...",
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icon_busy = fontawesome::fa_i("arrows-rotate",
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class = "fa-spin",
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"aria-hidden" = "true"
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),
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type = "secondary",
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auto_reset = TRUE
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),
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shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
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shiny::tags$br(),
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shiny::uiOutput(outputId = ns("plot_model"))
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),
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# plot_download_ui(ns("reg_plot_download"))
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shiny::tagList(
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shinyWidgets::noUiSliderInput(
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inputId = ns("plot_height"),
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label = "Plot height (mm)",
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min = 50,
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max = 300,
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value = 100,
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step = 1,
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format = shinyWidgets::wNumbFormat(decimals = 0),
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color = datamods:::get_primary_color()
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),
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shinyWidgets::noUiSliderInput(
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inputId = ns("plot_width"),
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label = "Plot width (mm)",
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min = 50,
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max = 300,
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value = 100,
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step = 1,
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format = shinyWidgets::wNumbFormat(decimals = 0),
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color = datamods:::get_primary_color()
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),
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shiny::selectInput(
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inputId = ns("plot_type"),
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label = "File format",
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shiny::radioButtons(
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inputId = ns("add_regression_p"),
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label = "Show p-value",
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inline = TRUE,
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selected = "yes",
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choices = list(
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"png",
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"tiff",
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"eps",
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"pdf",
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"jpeg",
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"svg"
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"Yes" = "yes",
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"No" = "no"
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)
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),
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shiny::br(),
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# Button
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shiny::downloadButton(
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outputId = ns("download_plot"),
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label = "Download plot",
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icon = shiny::icon("download")
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# shiny::tags$br(),
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# shiny::radioButtons(
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# inputId = ns("tbl_theme"),
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# label = "Show p-value",
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# inline = TRUE,
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# selected = "jama",
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# choices = list(
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# "JAMA" = "jama",
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# "Lancet" = "lancet",
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# "NEJM" = "nejm"
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# )
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# ),
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shiny::tags$br()
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)
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)
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),
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gt::gt_output(outputId = ns("table2"))
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)
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),
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bslib::nav_panel(
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title = "Coefficient plot",
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bslib::layout_sidebar(
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sidebar = bslib::sidebar(
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bslib::accordion(
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open = "acc_reg",
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multiple = FALSE,
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do.call(
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bslib::accordion_panel,
|
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c(
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list(
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value = "acc_plot",
|
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title = "Coefficient plot",
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icon = bsicons::bs_icon("bar-chart-steps"),
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shiny::tags$br(),
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shiny::uiOutput(outputId = ns("plot_model"))
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),
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# plot_download_ui(ns("reg_plot_download"))
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shiny::tagList(
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shinyWidgets::noUiSliderInput(
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inputId = ns("plot_height"),
|
||||
label = "Plot height (mm)",
|
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min = 50,
|
||||
max = 300,
|
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value = 100,
|
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step = 1,
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format = shinyWidgets::wNumbFormat(decimals = 0),
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color = datamods:::get_primary_color()
|
||||
),
|
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shinyWidgets::noUiSliderInput(
|
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inputId = ns("plot_width"),
|
||||
label = "Plot width (mm)",
|
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min = 50,
|
||||
max = 300,
|
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value = 100,
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step = 1,
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||||
format = shinyWidgets::wNumbFormat(decimals = 0),
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||||
color = datamods:::get_primary_color()
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),
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shiny::selectInput(
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||||
inputId = ns("plot_type"),
|
||||
label = "File format",
|
||||
choices = list(
|
||||
"png",
|
||||
"tiff",
|
||||
"eps",
|
||||
"pdf",
|
||||
"jpeg",
|
||||
"svg"
|
||||
)
|
||||
),
|
||||
shiny::br(),
|
||||
# Button
|
||||
shiny::downloadButton(
|
||||
outputId = ns("download_plot"),
|
||||
label = "Download plot",
|
||||
icon = shiny::icon("download")
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
),
|
||||
bslib::accordion_panel(
|
||||
value = "acc_checks",
|
||||
title = "Checks",
|
||||
icon = bsicons::bs_icon("clipboard-check"),
|
||||
shiny::uiOutput(outputId = ns("plot_checks"))
|
||||
)
|
||||
shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Regression table",
|
||||
gt::gt_output(outputId = ns("table2"))
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Coefficient plot",
|
||||
shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Model checks",
|
||||
shiny::plotOutput(outputId = ns("check"), height = "90vh")
|
||||
bslib::layout_sidebar(
|
||||
sidebar = bslib::sidebar(
|
||||
bslib::accordion(
|
||||
open = "acc_reg",
|
||||
multiple = FALSE,
|
||||
bslib::accordion_panel(
|
||||
value = "acc_checks",
|
||||
title = "Checks",
|
||||
icon = bsicons::bs_icon("clipboard-check"),
|
||||
shiny::uiOutput(outputId = ns("plot_checks"))
|
||||
)
|
||||
)
|
||||
),
|
||||
shiny::plotOutput(outputId = ns("check"), height = "90vh")
|
||||
)
|
||||
)
|
||||
)
|
||||
}
|
||||
|
|
|
|||
File diff suppressed because it is too large
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Add table
Reference in a new issue