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new ui

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Andreas Gammelgaard Damsbo 2025-07-03 16:19:51 +02:00
parent c7b879f458
commit ec5603d368
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4 changed files with 807 additions and 745 deletions
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164
R/data_plots.R
View file

@ -11,97 +11,96 @@
data_visuals_ui <- function(id, tab_title = "Plots", ...) { data_visuals_ui <- function(id, tab_title = "Plots", ...) {
ns <- shiny::NS(id) ns <- shiny::NS(id)
# bslib::navset_bar(
list( list(
bslib::layout_sidebar(
# Sidebar with a slider input sidebar = bslib::sidebar(
sidebar = bslib::sidebar( bslib::accordion(
bslib::accordion( multiple = FALSE,
multiple = FALSE, bslib::accordion_panel(
bslib::accordion_panel( title = "Creating plot",
title = "Creating plot", icon = bsicons::bs_icon("graph-up"),
icon = bsicons::bs_icon("graph-up"), shiny::uiOutput(outputId = ns("primary")),
shiny::uiOutput(outputId = ns("primary")), shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'), shiny::tags$br(),
shiny::tags$br(), shiny::uiOutput(outputId = ns("type")),
shiny::uiOutput(outputId = ns("type")), shiny::uiOutput(outputId = ns("secondary")),
shiny::uiOutput(outputId = ns("secondary")), shiny::uiOutput(outputId = ns("tertiary")),
shiny::uiOutput(outputId = ns("tertiary")), shiny::br(),
shiny::br(), shiny::actionButton(
shiny::actionButton( inputId = ns("act_plot"),
inputId = ns("act_plot"), label = "Plot",
label = "Plot", width = "100%",
width = "100%", icon = shiny::icon("palette"),
icon = shiny::icon("palette"), disabled = FALSE
disabled = FALSE ),
shiny::helpText('Adjust settings, then press "Plot".')
), ),
shiny::helpText('Adjust settings, then press "Plot".') bslib::accordion_panel(
), title = "Download",
# bslib::accordion_panel( icon = bsicons::bs_icon("download"),
# title = "Advanced", shinyWidgets::noUiSliderInput(
# icon = bsicons::bs_icon("gear") inputId = ns("height_slide"),
# ), label = "Plot height (mm)",
bslib::accordion_panel( min = 50,
title = "Download", max = 300,
icon = bsicons::bs_icon("download"), value = 100,
shinyWidgets::noUiSliderInput( step = 1,
inputId = ns("height_slide"), format = shinyWidgets::wNumbFormat(decimals = 0),
label = "Plot height (mm)", color = datamods:::get_primary_color(),
min = 50, inline = TRUE
max = 300, ),
value = 100, # shiny::numericInput(
step = 1, # inputId = ns("height_numeric"),
format = shinyWidgets::wNumbFormat(decimals = 0), # label = "Plot height (mm)",
color = datamods:::get_primary_color(), # min = 50,
inline = TRUE # max = 300,
), # value = 100
# shiny::numericInput( # ),
# inputId = ns("height_numeric"), shinyWidgets::noUiSliderInput(
# label = "Plot height (mm)", inputId = ns("width"),
# min = 50, label = "Plot width (mm)",
# max = 300, min = 50,
# value = 100 max = 300,
# ), value = 100,
shinyWidgets::noUiSliderInput( step = 1,
inputId = ns("width"), format = shinyWidgets::wNumbFormat(decimals = 0),
label = "Plot width (mm)", color = datamods:::get_primary_color()
min = 50, ),
max = 300, shiny::selectInput(
value = 100, inputId = ns("plot_type"),
step = 1, label = "File format",
format = shinyWidgets::wNumbFormat(decimals = 0), choices = list(
color = datamods:::get_primary_color() "png",
), "tiff",
shiny::selectInput( "eps",
inputId = ns("plot_type"), "pdf",
label = "File format", "jpeg",
choices = list( "svg"
"png", )
"tiff", ),
"eps", shiny::br(),
"pdf", # Button
"jpeg", shiny::downloadButton(
"svg" outputId = ns("download_plot"),
label = "Download plot",
icon = shiny::icon("download")
) )
),
shiny::br(),
# Button
shiny::downloadButton(
outputId = ns("download_plot"),
label = "Download plot",
icon = shiny::icon("download")
) )
) ),
) shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a(
), href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
bslib::nav_panel( "View notes in new tab",
title = tab_title, target = "_blank",
rel = "noopener noreferrer"
))
),
shiny::plotOutput(ns("plot"), height = "70vh"), shiny::plotOutput(ns("plot"), height = "70vh"),
shiny::tags$br(), shiny::tags$br(),
shiny::tags$br(), shiny::tags$br(),
shiny::htmlOutput(outputId = ns("code_plot")) shiny::htmlOutput(outputId = ns("code_plot"))
) )
) )
# )
} }
@ -725,6 +724,7 @@ get_label <- function(data, var = NULL) {
#' paste(sample(letters[1:10], 100, TRUE), collapse = "") |> line_break(force = TRUE) #' paste(sample(letters[1:10], 100, TRUE), collapse = "") |> line_break(force = TRUE)
line_break <- function(data, lineLength = 20, force = FALSE) { line_break <- function(data, lineLength = 20, force = FALSE) {
if (isTRUE(force)) { if (isTRUE(force)) {
## This eats some letters when splitting a sentence... ??
gsub(paste0("(.{1,", lineLength, "})(\\s|[[:alnum:]])"), "\\1\n", data) gsub(paste0("(.{1,", lineLength, "})(\\s|[[:alnum:]])"), "\\1\n", data)
} else { } else {
paste(strwrap(data, lineLength), collapse = "\n") paste(strwrap(data, lineLength), collapse = "\n")
@ -746,7 +746,7 @@ line_break <- function(data, lineLength = 20, force = FALSE) {
wrap_plot_list <- function(data, wrap_plot_list <- function(data,
tag_levels = NULL, tag_levels = NULL,
title = NULL, title = NULL,
axis.font.family=NULL, axis.font.family = NULL,
...) { ...) {
if (ggplot2::is_ggplot(data[[1]])) { if (ggplot2::is_ggplot(data[[1]])) {
if (length(data) > 1) { if (length(data) > 1) {

33
R/missings-module.R
View file

@ -44,14 +44,7 @@ data_missings_server <- function(id,
tryCatch( tryCatch(
{ {
if (!is.null(by_var) && by_var != "" && by_var %in% names(df_tbl)) { out <- compare_missings(df_tbl,by_var)
df_tbl[[by_var]] <- ifelse(is.na(df_tbl[[by_var]]), "Missing", "Non-missing")
out <- gtsummary::tbl_summary(df_tbl, by = by_var) |>
gtsummary::add_p()
} else {
out <- gtsummary::tbl_summary(df_tbl)
}
}, },
error = function(err) { error = function(err) {
showNotification(paste0("Error: ", err), type = "err") showNotification(paste0("Error: ", err), type = "err")
@ -129,10 +122,22 @@ missing_demo_app <- function() {
missing_demo_app() missing_demo_app()
#' Pairwise comparison of missings across covariables
#'
#' @param data data frame
#' @param by_var variable to stratify by missingness
#'
#' @returns gtsummary list object
#' @export
#'
compare_missings <- function(data,by_var){
if (!is.null(by_var) && by_var != "" && by_var %in% names(data)) {
data[[by_var]] <- ifelse(is.na(data[[by_var]]), "Missing", "Non-missing")
out <- gtsummary::tbl_summary(data, by = by_var) |>
gtsummary::add_p()
} else {
out <- gtsummary::tbl_summary(data)
}
out
}

292
R/regression-module.R
View file

@ -44,155 +44,173 @@ regression_ui <- function(id, ...) {
ns <- shiny::NS(id) ns <- shiny::NS(id)
shiny::tagList( shiny::tagList(
title = "", # title = "",
sidebar = bslib::sidebar( bslib::nav_panel(
shiny::uiOutput(outputId = ns("data_info"), inline = TRUE), title = "Regression table",
bslib::accordion( bslib::layout_sidebar(
open = "acc_reg", sidebar = bslib::sidebar(
multiple = FALSE, shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
bslib::accordion_panel( bslib::accordion(
value = "acc_reg", open = "acc_reg",
title = "Regression", multiple = FALSE,
icon = bsicons::bs_icon("calculator"), bslib::accordion_panel(
shiny::uiOutput(outputId = ns("outcome_var")), value = "acc_reg",
# shiny::selectInput( title = "Regression",
# inputId = "design", icon = bsicons::bs_icon("calculator"),
# label = "Study design", shiny::uiOutput(outputId = ns("outcome_var")),
# selected = "no", # shiny::selectInput(
# inline = TRUE, # inputId = "design",
# choices = list( # label = "Study design",
# "Cross-sectional" = "cross-sectional" # selected = "no",
# ) # inline = TRUE,
# ), # choices = list(
shiny::uiOutput(outputId = ns("regression_type")), # "Cross-sectional" = "cross-sectional"
shiny::radioButtons( # )
inputId = ns("all"), # ),
label = "Specify covariables", shiny::uiOutput(outputId = ns("regression_type")),
inline = TRUE, selected = 2, shiny::radioButtons(
choiceNames = c( inputId = ns("all"),
"Yes", label = "Specify covariables",
"No" inline = TRUE, selected = 2,
), choiceNames = c(
choiceValues = c(1, 2) "Yes",
), "No"
shiny::conditionalPanel( ),
condition = "input.all==1", choiceValues = c(1, 2)
shiny::uiOutput(outputId = ns("regression_vars")), ),
shiny::helpText("If none are selected, all are included."), shiny::conditionalPanel(
shiny::tags$br(), condition = "input.all==1",
ns = ns shiny::uiOutput(outputId = ns("regression_vars")),
), shiny::helpText("If none are selected, all are included."),
bslib::input_task_button( shiny::tags$br(),
id = ns("load"), ns = ns
label = "Analyse", ),
icon = bsicons::bs_icon("pencil"), bslib::input_task_button(
label_busy = "Working...", id = ns("load"),
icon_busy = fontawesome::fa_i("arrows-rotate", label = "Analyse",
class = "fa-spin", icon = bsicons::bs_icon("pencil"),
"aria-hidden" = "true" label_busy = "Working...",
), icon_busy = fontawesome::fa_i("arrows-rotate",
type = "secondary", class = "fa-spin",
auto_reset = TRUE "aria-hidden" = "true"
), ),
shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."), type = "secondary",
shiny::tags$br(), auto_reset = TRUE
shiny::radioButtons( ),
inputId = ns("add_regression_p"), shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
label = "Show p-value",
inline = TRUE,
selected = "yes",
choices = list(
"Yes" = "yes",
"No" = "no"
)
),
# shiny::tags$br(),
# shiny::radioButtons(
# inputId = ns("tbl_theme"),
# label = "Show p-value",
# inline = TRUE,
# selected = "jama",
# choices = list(
# "JAMA" = "jama",
# "Lancet" = "lancet",
# "NEJM" = "nejm"
# )
# ),
shiny::tags$br()
),
do.call(
bslib::accordion_panel,
c(
list(
value = "acc_plot",
title = "Coefficient plot",
icon = bsicons::bs_icon("bar-chart-steps"),
shiny::tags$br(), shiny::tags$br(),
shiny::uiOutput(outputId = ns("plot_model")) shiny::radioButtons(
), inputId = ns("add_regression_p"),
# plot_download_ui(ns("reg_plot_download")) label = "Show p-value",
shiny::tagList( inline = TRUE,
shinyWidgets::noUiSliderInput( selected = "yes",
inputId = ns("plot_height"),
label = "Plot height (mm)",
min = 50,
max = 300,
value = 100,
step = 1,
format = shinyWidgets::wNumbFormat(decimals = 0),
color = datamods:::get_primary_color()
),
shinyWidgets::noUiSliderInput(
inputId = ns("plot_width"),
label = "Plot width (mm)",
min = 50,
max = 300,
value = 100,
step = 1,
format = shinyWidgets::wNumbFormat(decimals = 0),
color = datamods:::get_primary_color()
),
shiny::selectInput(
inputId = ns("plot_type"),
label = "File format",
choices = list( choices = list(
"png", "Yes" = "yes",
"tiff", "No" = "no"
"eps",
"pdf",
"jpeg",
"svg"
) )
), ),
shiny::br(), # shiny::tags$br(),
# Button # shiny::radioButtons(
shiny::downloadButton( # inputId = ns("tbl_theme"),
outputId = ns("download_plot"), # label = "Show p-value",
label = "Download plot", # inline = TRUE,
icon = shiny::icon("download") # selected = "jama",
# choices = list(
# "JAMA" = "jama",
# "Lancet" = "lancet",
# "NEJM" = "nejm"
# )
# ),
shiny::tags$br()
)
)
),
gt::gt_output(outputId = ns("table2"))
)
),
bslib::nav_panel(
title = "Coefficient plot",
bslib::layout_sidebar(
sidebar = bslib::sidebar(
bslib::accordion(
open = "acc_reg",
multiple = FALSE,
do.call(
bslib::accordion_panel,
c(
list(
value = "acc_plot",
title = "Coefficient plot",
icon = bsicons::bs_icon("bar-chart-steps"),
shiny::tags$br(),
shiny::uiOutput(outputId = ns("plot_model"))
),
# plot_download_ui(ns("reg_plot_download"))
shiny::tagList(
shinyWidgets::noUiSliderInput(
inputId = ns("plot_height"),
label = "Plot height (mm)",
min = 50,
max = 300,
value = 100,
step = 1,
format = shinyWidgets::wNumbFormat(decimals = 0),
color = datamods:::get_primary_color()
),
shinyWidgets::noUiSliderInput(
inputId = ns("plot_width"),
label = "Plot width (mm)",
min = 50,
max = 300,
value = 100,
step = 1,
format = shinyWidgets::wNumbFormat(decimals = 0),
color = datamods:::get_primary_color()
),
shiny::selectInput(
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( shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
value = "acc_checks",
title = "Checks",
icon = bsicons::bs_icon("clipboard-check"),
shiny::uiOutput(outputId = ns("plot_checks"))
)
) )
), ),
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( bslib::nav_panel(
title = "Model checks", 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")
)
) )
) )
} }

1063
inst/apps/FreesearchR/app.R
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