mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 01:49:39 +02:00
updated docs + boxplot
This commit is contained in:
parent
04784a7a24
commit
111393c73f
23 changed files with 908 additions and 306 deletions
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@ -1,6 +1,6 @@
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^renv$
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^renv\.lock$
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^freesearcheR\.Rproj$
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^FreesearchR\.Rproj$
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^\.Rproj\.user$
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^LICENSE\.md$
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^dev$
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@ -80,6 +80,6 @@ Suggests:
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rsconnect,
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knitr,
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rmarkdown
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URL: https://github.com/agdamsbo/freesearcheR, https://agdamsbo.github.io/freesearcheR/
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BugReports: https://github.com/agdamsbo/freesearcheR/issues
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URL: https://github.com/agdamsbo/FreesearchR, https://agdamsbo.github.io/FreesearchR/
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BugReports: https://github.com/agdamsbo/FreesearchR/issues
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VignetteBuilder: knitr
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@ -5,6 +5,8 @@ S3method(plot,tbl_regression)
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export(add_class_icon)
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export(add_sparkline)
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export(all_but)
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export(allign_axes)
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export(append_list)
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export(argsstring2list)
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export(baseline_table)
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export(clean_date)
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@ -49,6 +51,7 @@ export(is_datetime)
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export(is_valid_redcap_url)
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export(is_valid_token)
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export(launch_FreesearchR)
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export(limit_log)
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export(line_break)
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export(m_datafileUI)
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export(m_redcap_readServer)
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@ -85,6 +88,7 @@ export(specify_qmd_format)
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export(subset_types)
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export(supported_functions)
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export(supported_plots)
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export(symmetrical_scale_x_log10)
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export(tbl_merge)
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export(update_factor_server)
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export(update_factor_ui)
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@ -95,6 +99,7 @@ export(vertical_stacked_bars)
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export(wide2long)
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export(winbox_cut_variable)
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export(winbox_update_factor)
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export(wrap_plot_list)
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export(write_quarto)
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importFrom(classInt,classIntervals)
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importFrom(data.table,as.data.table)
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4
NEWS.md
4
NEWS.md
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@ -1,8 +1,8 @@
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# freesearcheR 25.3.2
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# FreesearchR 25.3.2
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Focus is on polish and improved ui/ux.
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First steps towards an updated name (will be FreesearchR), with renamed repository. This may introduce some breaking chances for others calling or installing the package. No future changes are planned. A complete transition is planned before attending and presenting a poster at the European Stroke Organisation COnference 2025 in May.
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Updating name (will be FreesearchR), with renamed repository and some graphics are comng. This may introduce some breaking chances for others calling or installing the package. No future changes are planned. A complete transition is planned before attending and presenting a poster at the European Stroke Organisation Conference 2025 in May.
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Testing file upload conducted and improved.
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@ -1 +1 @@
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app_version <- function()'250318_0827'
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app_version <- function()'250319_1306'
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@ -102,13 +102,16 @@ library(shiny)
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#' f <- d_t |> cut(2)
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#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "03:02:20", NA)) |> cut(breaks = lubridate::as_datetime(c(hms::as_hms(levels(f)), hms::as_hms(max(d_t, na.rm = TRUE) + 1))), right = FALSE)
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cut.hms <- function(x, breaks, ...) {
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## as_hms keeps returning warnings on tz(); ignored
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suppressWarnings({
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if (hms::is_hms(breaks)) {
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breaks <- lubridate::as_datetime(breaks, tz = "UTC")
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breaks <- lubridate::as_datetime(breaks)
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}
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x <- lubridate::as_datetime(x, tz = "UTC")
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x <- lubridate::as_datetime(x)
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out <- cut.POSIXt(x, breaks = breaks, ...)
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attr(out, which = "brks") <- hms::as_hms(lubridate::as_datetime(attr(out, which = "brks")))
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attr(out, which = "levels") <- as.character(hms::as_hms(lubridate::as_datetime(attr(out, which = "levels"))))
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})
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out
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}
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@ -59,27 +59,7 @@ data_import_server <- function(id) {
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id = ns("file_import"),
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show_data_in = "popup",
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trigger_return = "change",
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return_class = "data.frame",
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read_fns = list(
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ods = import_ods,
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dta = function(file) {
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haven::read_dta(
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file = file,
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.name_repair = "unique_quiet"
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)
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},
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csv = import_delim,
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tsv = import_delim,
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txt = import_delim,
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xls = import_xls,
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xlsx = import_xls,
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rds = function(file) {
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readr::read_rds(
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file = file,
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name_repair = "unique_quiet"
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)
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}
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)
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return_class = "data.frame"
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)
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shiny::observeEvent(data_file$data(), {
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178
R/data_plots.R
178
R/data_plots.R
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@ -112,6 +112,99 @@ data_visuals_server <- function(id,
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plot = NULL
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)
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# ## --- New attempt
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#
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# rv$plot.params <- shiny::reactive({
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# get_plot_options(input$type) |> purrr::pluck(1)
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# })
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#
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# c(output,
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# list(shiny::renderUI({
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# columnSelectInput(
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# inputId = ns("primary"),
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# data = data,
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# placeholder = "Select variable",
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# label = "Response variable",
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# multiple = FALSE
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# )
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# }),
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# shiny::renderUI({
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# shiny::req(input$primary)
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# # browser()
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#
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# if (!input$primary %in% names(data())) {
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# plot_data <- data()[1]
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# } else {
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# plot_data <- data()[input$primary]
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# }
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#
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# plots <- possible_plots(
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# data = plot_data
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# )
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#
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# plots_named <- get_plot_options(plots) |>
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# lapply(\(.x){
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# stats::setNames(.x$descr, .x$note)
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# })
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#
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# vectorSelectInput(
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# inputId = ns("type"),
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# selected = NULL,
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# label = shiny::h4("Plot type"),
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# choices = Reduce(c, plots_named),
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# multiple = FALSE
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# )
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# }),
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# shiny::renderUI({
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# shiny::req(input$type)
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#
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# cols <- c(
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# rv$plot.params()[["secondary.extra"]],
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# all_but(
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# colnames(subset_types(
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# data(),
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# rv$plot.params()[["secondary.type"]]
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# )),
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# input$primary
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# )
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# )
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#
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# columnSelectInput(
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# inputId = ns("secondary"),
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# data = data,
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# selected = cols[1],
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# placeholder = "Please select",
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# label = if (isTRUE(rv$plot.params()[["secondary.multi"]])) "Additional variables" else "Secondary variable",
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# multiple = rv$plot.params()[["secondary.multi"]],
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# maxItems = rv$plot.params()[["secondary.max"]],
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# col_subset = cols,
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# none_label = "No variable"
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# )
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# }),
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# shiny::renderUI({
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# shiny::req(input$type)
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# columnSelectInput(
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# inputId = ns("tertiary"),
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# data = data,
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# placeholder = "Please select",
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# label = "Grouping variable",
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# multiple = FALSE,
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# col_subset = c(
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# "none",
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# all_but(
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# colnames(subset_types(
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# data(),
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# rv$plot.params()[["tertiary.type"]]
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# )),
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# input$primary,
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# input$secondary
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# )
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# ),
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# none_label = "No stratification"
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# )
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# })
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# )|> setNames(c("primary","type","secondary","tertiary")),keep.null = TRUE)
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output$primary <- shiny::renderUI({
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columnSelectInput(
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inputId = ns("primary"),
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@ -364,6 +457,16 @@ supported_plots <- function() {
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tertiary.type = c("dichotomous", "ordinal"),
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secondary.extra = NULL
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),
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plot_box = list(
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fun = "plot_box",
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descr = "Box plot",
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note = "A classic way to plot data distribution by groups",
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primary.type = c("continuous", "dichotomous", "ordinal"),
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secondary.type = c("dichotomous", "ordinal"),
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secondary.multi = FALSE,
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tertiary.type = c("dichotomous", "ordinal"),
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secondary.extra = "none"
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),
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plot_euler = list(
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fun = "plot_euler",
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descr = "Euler diagram",
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@ -535,18 +638,49 @@ line_break <- function(data, lineLength = 20, fixed = FALSE) {
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}
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wrap_plot_list <- function(data) {
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if (length(data) > 1) {
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out <- data |>
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allign_axes() |>
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patchwork::wrap_plots(guides = "collect", axes = "collect", axis_titles = "collect")
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#' Wrapping
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#'
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#' @param data list of ggplot2 objects
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#' @param tag_levels passed to patchwork::plot_annotation if given. Default is NULL
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#'
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#' @returns list of ggplot2 objects
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#' @export
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#'
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wrap_plot_list <- function(data, tag_levels = NULL) {
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if (ggplot2::is.ggplot(data[[1]])) {
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if (length(data) > 1) {
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out <- data |>
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(\(.x){
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if (rlang::is_named(.x)) {
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purrr::imap(.x, \(.y, .i){
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.y + ggplot2::ggtitle(.i)
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})
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} else {
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.x
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}
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})() |>
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allign_axes() |>
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patchwork::wrap_plots(guides = "collect", axes = "collect", axis_titles = "collect")
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if (!is.null(tag_levels)) {
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out <- out + patchwork::plot_annotation(tag_levels = tag_levels)
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}
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} else {
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out <- data
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}
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} else {
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out <- data
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cli::cli_abort("Can only wrap lists of {.cls ggplot} objects")
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}
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out
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}
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#' Alligns axes between plots
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#'
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#' @param ... ggplot2 objects or list of ggplot2 objects
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#'
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#' @returns list of ggplot2 objects
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#' @export
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#'
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allign_axes <- function(...) {
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# https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object
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# https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150
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@ -558,16 +692,30 @@ allign_axes <- function(...) {
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cli::cli_abort("Can only align {.cls ggplot} objects or a list of them")
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}
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# browser()
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yr <- purrr::map(p, ~ ggplot2::layer_scales(.x)$y$get_limits()) |>
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unlist() |>
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range() |>
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unique()
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yr <- clean_common_axis(p, "y")
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xr <- purrr::map(p, ~ ggplot2::layer_scales(.x)$x$get_limits()) |>
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unlist() |>
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range() |>
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unique()
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xr <- clean_common_axis(p, "x")
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p |> purrr::map(~ .x + ggplot2::xlim(xr) + ggplot2::ylim(yr))
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}
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#' Extract and clean axis ranges
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#'
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#' @param p plot
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#' @param axis axis. x or y.
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#'
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#' @returns vector
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#' @export
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#'
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clean_common_axis <- function(p, axis) {
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purrr::map(p, ~ ggplot2::layer_scales(.x)[[axis]]$get_limits()) |>
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unlist() |>
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(\(.x){
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if (is.numeric(.x)) {
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range(.x)
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} else {
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.x
|
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}
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})() |>
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unique()
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}
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|
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|
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@ -215,7 +215,9 @@ default_parsing <- function(data) {
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out <- data |>
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REDCapCAST::parse_data() |>
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REDCapCAST::as_factor() |>
|
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REDCapCAST::numchar2fct()
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REDCapCAST::numchar2fct(numeric.threshold = 8,character.throshold = 10) |>
|
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REDCapCAST::as_logical() |>
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REDCapCAST::fct_drop()
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|
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purrr::map2(out,name_labels,\(.x,.l){
|
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if (!(is.na(.l) | .l=="")) {
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|
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@ -275,6 +277,7 @@ remove_empty_cols <- function(data,cutoff=.7){
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#' @param index index name
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#'
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#' @returns list
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#' @export
|
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#'
|
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#' @examples
|
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#' ls_d <- list(test=c(1:20))
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|
|
|
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80
R/plot_box.R
Normal file
80
R/plot_box.R
Normal file
|
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@ -0,0 +1,80 @@
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#' Beautiful box plot(s)
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#'
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#' @returns ggplot2 object
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#' @export
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#'
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#' @name data-plots
|
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#'
|
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#' @examples
|
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#' mtcars |> plot_box(x = "mpg", y = "cyl", z = "gear")
|
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#' mtcars |>
|
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#' default_parsing() |>
|
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#' plot_box(x = "mpg", y = "cyl", z = "gear")
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plot_box <- function(data, x, y, z = NULL) {
|
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if (!is.null(z)) {
|
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ds <- split(data, data[z])
|
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} else {
|
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ds <- list(data)
|
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}
|
||||
|
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out <- lapply(ds, \(.ds){
|
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plot_box_single(
|
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data = .ds,
|
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x = x,
|
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y = y
|
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)
|
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})
|
||||
|
||||
wrap_plot_list(out)
|
||||
# patchwork::wrap_plots(out,guides = "collect")
|
||||
}
|
||||
|
||||
|
||||
|
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|
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#' Create nice box-plots
|
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#'
|
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#' @name data-plots
|
||||
#'
|
||||
#' @returns
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' mtcars |> plot_box_single("mpg","cyl")
|
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plot_box_single <- function(data, x, y=NULL, seed = 2103) {
|
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set.seed(seed)
|
||||
|
||||
if (is.null(y)) {
|
||||
y <- "All"
|
||||
data[[y]] <- y
|
||||
}
|
||||
|
||||
discrete <- !outcome_type(data[[y]]) %in% "continuous"
|
||||
|
||||
data |>
|
||||
ggplot2::ggplot(ggplot2::aes(x = !!dplyr::sym(x), y = !!dplyr::sym(y), fill = !!dplyr::sym(y), group = !!dplyr::sym(y))) +
|
||||
ggplot2::geom_boxplot(linewidth = 1.8, outliers = FALSE) +
|
||||
## THis could be optional in future
|
||||
ggplot2::geom_jitter(color = "black", size = 2, alpha = 0.9) +
|
||||
ggplot2::coord_flip() +
|
||||
viridis::scale_fill_viridis(discrete = discrete, option = "D") +
|
||||
# ggplot2::theme_void() +
|
||||
ggplot2::theme_bw(base_size = 24) +
|
||||
ggplot2::theme(
|
||||
legend.position = "none",
|
||||
# panel.grid.major = element_blank(),
|
||||
# panel.grid.minor = element_blank(),
|
||||
# axis.text.y = element_blank(),
|
||||
# axis.title.y = element_blank(),
|
||||
# text = ggplot2::element_text(size = 20),
|
||||
# axis.text = ggplot2::element_blank(),
|
||||
# plot.title = element_blank(),
|
||||
panel.background = ggplot2::element_rect(fill = "white"),
|
||||
plot.background = ggplot2::element_rect(fill = "white"),
|
||||
panel.border = ggplot2::element_blank(),
|
||||
panel.grid.major = ggplot2::element_blank(),
|
||||
panel.grid.minor = ggplot2::element_blank(),
|
||||
axis.line = ggplot2::element_line(colour = "black"),
|
||||
axis.ticks = ggplot2::element_line(colour = "black")
|
||||
)
|
||||
}
|
||||
|
|
@ -78,9 +78,6 @@ ggeulerr <- function(
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#' mtcars |> plot_euler("vs", "am", seed = 1)
|
||||
plot_euler <- function(data, x, y, z = NULL, seed = 2103) {
|
||||
set.seed(seed = seed)
|
||||
|
||||
# data <- data[c(...,z)]
|
||||
|
||||
if (!is.null(z)) {
|
||||
ds <- split(data, data[z])
|
||||
} else {
|
||||
|
|
@ -93,6 +90,7 @@ plot_euler <- function(data, x, y, z = NULL, seed = 2103) {
|
|||
plot_euler_single()
|
||||
})
|
||||
|
||||
# names(out)
|
||||
wrap_plot_list(out)
|
||||
# patchwork::wrap_plots(out, guides = "collect")
|
||||
}
|
||||
|
|
@ -116,7 +114,7 @@ plot_euler_single <- function(data) {
|
|||
ggeulerr(shape = "circle") +
|
||||
ggplot2::theme_void() +
|
||||
ggplot2::theme(
|
||||
legend.position = "right",
|
||||
legend.position = "none",
|
||||
# panel.grid.major = element_blank(),
|
||||
# panel.grid.minor = element_blank(),
|
||||
# axis.text.y = element_blank(),
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ plot.tbl_regression <- function(x,
|
|||
# gtsummary:::check_scalar_logical(remove_reference_rows)
|
||||
|
||||
df_coefs <- x$table_body
|
||||
browser()
|
||||
|
||||
if (isTRUE(remove_header_rows)) {
|
||||
df_coefs <- df_coefs |> dplyr::filter(!header_row %in% TRUE)
|
||||
}
|
||||
|
|
@ -48,22 +48,16 @@ plot.tbl_regression <- function(x,
|
|||
if (plot_ref == TRUE){
|
||||
df_coefs[df_coefs$var_type == "categorical" & is.na(df_coefs$reference_row),"estimate"] <- if (x$inputs$exponentiate) 1 else 0}
|
||||
|
||||
df_coefs |>
|
||||
p <- df_coefs |>
|
||||
ggstats::ggcoef_plot(exponentiate = x$inputs$exponentiate, ...)
|
||||
|
||||
if (x$inputs$exponentiate){
|
||||
p <- symmetrical_scale_x_log10(p)
|
||||
}
|
||||
p
|
||||
}
|
||||
|
||||
|
||||
# default_parsing(mtcars) |> lapply(class)
|
||||
#
|
||||
# purrr::imap(mtcars,\(.x,.i){
|
||||
# if (.i %in% c("vs","am","gear","carb")){
|
||||
# as.factor(.x)
|
||||
# } else .x
|
||||
# }) |> dplyr::bind_cols()
|
||||
#
|
||||
#
|
||||
|
||||
|
||||
#' Wrapper to pivot gtsummary table data to long for plotting
|
||||
#'
|
||||
#' @param list a custom regression models list
|
||||
|
|
@ -103,3 +97,47 @@ merge_long <- function(list, model.names) {
|
|||
|
||||
l_merged
|
||||
}
|
||||
|
||||
|
||||
#' Easily round log scale limits for nice plots
|
||||
#'
|
||||
#' @param data data
|
||||
#' @param fun rounding function (floor/ceiling)
|
||||
#' @param ... ignored
|
||||
#'
|
||||
#' @returns numeric vector
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' limit_log(-.1,floor)
|
||||
#' limit_log(.1,ceiling)
|
||||
#' limit_log(-2.1,ceiling)
|
||||
#' limit_log(2.1,ceiling)
|
||||
limit_log <- function(data,fun,...){
|
||||
fun(10^-floor(data)*10^data)/10^-floor(data)
|
||||
}
|
||||
|
||||
#' Ensure symmetrical plot around 1 on a logarithmic x scale for ratio plots
|
||||
#'
|
||||
#' @param plot ggplot2 plot
|
||||
#' @param breaks breaks used and mirrored
|
||||
#' @param ... ignored
|
||||
#'
|
||||
#' @returns ggplot2 object
|
||||
#' @export
|
||||
#'
|
||||
symmetrical_scale_x_log10 <- function(plot,breaks=c(1,2,3,5,10),...){
|
||||
rx <- ggplot2::layer_scales(plot)$x$get_limits()
|
||||
|
||||
x_min <- floor(10*rx[1])/10
|
||||
x_max <- ceiling(10*rx[2])/10
|
||||
|
||||
rx_min <- limit_log(rx[1],floor)
|
||||
rx_max <- limit_log(rx[2],ceiling)
|
||||
|
||||
max_abs_x <- max(abs(c(x_min,x_max)))
|
||||
|
||||
ticks <- log10(breaks)+(ceiling(max_abs_x)-1)
|
||||
browser()
|
||||
plot + ggplot2::scale_x_log10(limits=c(rx_min,rx_max),breaks=create_log_tics(10^ticks[ticks<=max_abs_x]))
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
url: https://agdamsbo.github.io/freesearcheR/
|
||||
url: https://agdamsbo.github.io/FreesearchR/
|
||||
template:
|
||||
bslib:
|
||||
version: 5
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/freesearcheR/functions.R
|
||||
#### Current file: /Users/au301842/FreesearchR/inst/apps/FreesearchR/functions.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -10,7 +10,7 @@
|
|||
#### Current file: R//app_version.R
|
||||
########
|
||||
|
||||
app_version <- function()'250318_0827'
|
||||
app_version <- function()'250319_1306'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -554,13 +554,16 @@ library(shiny)
|
|||
#' f <- d_t |> cut(2)
|
||||
#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "03:02:20", NA)) |> cut(breaks = lubridate::as_datetime(c(hms::as_hms(levels(f)), hms::as_hms(max(d_t, na.rm = TRUE) + 1))), right = FALSE)
|
||||
cut.hms <- function(x, breaks, ...) {
|
||||
## as_hms keeps returning warnings on tz(); ignored
|
||||
suppressWarnings({
|
||||
if (hms::is_hms(breaks)) {
|
||||
breaks <- lubridate::as_datetime(breaks, tz = "UTC")
|
||||
breaks <- lubridate::as_datetime(breaks)
|
||||
}
|
||||
x <- lubridate::as_datetime(x, tz = "UTC")
|
||||
x <- lubridate::as_datetime(x)
|
||||
out <- cut.POSIXt(x, breaks = breaks, ...)
|
||||
attr(out, which = "brks") <- hms::as_hms(lubridate::as_datetime(attr(out, which = "brks")))
|
||||
attr(out, which = "levels") <- as.character(hms::as_hms(lubridate::as_datetime(attr(out, which = "levels"))))
|
||||
})
|
||||
out
|
||||
}
|
||||
|
||||
|
|
@ -1206,6 +1209,99 @@ data_visuals_server <- function(id,
|
|||
plot = NULL
|
||||
)
|
||||
|
||||
# ## --- New attempt
|
||||
#
|
||||
# rv$plot.params <- shiny::reactive({
|
||||
# get_plot_options(input$type) |> purrr::pluck(1)
|
||||
# })
|
||||
#
|
||||
# c(output,
|
||||
# list(shiny::renderUI({
|
||||
# columnSelectInput(
|
||||
# inputId = ns("primary"),
|
||||
# data = data,
|
||||
# placeholder = "Select variable",
|
||||
# label = "Response variable",
|
||||
# multiple = FALSE
|
||||
# )
|
||||
# }),
|
||||
# shiny::renderUI({
|
||||
# shiny::req(input$primary)
|
||||
# # browser()
|
||||
#
|
||||
# if (!input$primary %in% names(data())) {
|
||||
# plot_data <- data()[1]
|
||||
# } else {
|
||||
# plot_data <- data()[input$primary]
|
||||
# }
|
||||
#
|
||||
# plots <- possible_plots(
|
||||
# data = plot_data
|
||||
# )
|
||||
#
|
||||
# plots_named <- get_plot_options(plots) |>
|
||||
# lapply(\(.x){
|
||||
# stats::setNames(.x$descr, .x$note)
|
||||
# })
|
||||
#
|
||||
# vectorSelectInput(
|
||||
# inputId = ns("type"),
|
||||
# selected = NULL,
|
||||
# label = shiny::h4("Plot type"),
|
||||
# choices = Reduce(c, plots_named),
|
||||
# multiple = FALSE
|
||||
# )
|
||||
# }),
|
||||
# shiny::renderUI({
|
||||
# shiny::req(input$type)
|
||||
#
|
||||
# cols <- c(
|
||||
# rv$plot.params()[["secondary.extra"]],
|
||||
# all_but(
|
||||
# colnames(subset_types(
|
||||
# data(),
|
||||
# rv$plot.params()[["secondary.type"]]
|
||||
# )),
|
||||
# input$primary
|
||||
# )
|
||||
# )
|
||||
#
|
||||
# columnSelectInput(
|
||||
# inputId = ns("secondary"),
|
||||
# data = data,
|
||||
# selected = cols[1],
|
||||
# placeholder = "Please select",
|
||||
# label = if (isTRUE(rv$plot.params()[["secondary.multi"]])) "Additional variables" else "Secondary variable",
|
||||
# multiple = rv$plot.params()[["secondary.multi"]],
|
||||
# maxItems = rv$plot.params()[["secondary.max"]],
|
||||
# col_subset = cols,
|
||||
# none_label = "No variable"
|
||||
# )
|
||||
# }),
|
||||
# shiny::renderUI({
|
||||
# shiny::req(input$type)
|
||||
# columnSelectInput(
|
||||
# inputId = ns("tertiary"),
|
||||
# data = data,
|
||||
# placeholder = "Please select",
|
||||
# label = "Grouping variable",
|
||||
# multiple = FALSE,
|
||||
# col_subset = c(
|
||||
# "none",
|
||||
# all_but(
|
||||
# colnames(subset_types(
|
||||
# data(),
|
||||
# rv$plot.params()[["tertiary.type"]]
|
||||
# )),
|
||||
# input$primary,
|
||||
# input$secondary
|
||||
# )
|
||||
# ),
|
||||
# none_label = "No stratification"
|
||||
# )
|
||||
# })
|
||||
# )|> setNames(c("primary","type","secondary","tertiary")),keep.null = TRUE)
|
||||
|
||||
output$primary <- shiny::renderUI({
|
||||
columnSelectInput(
|
||||
inputId = ns("primary"),
|
||||
|
|
@ -1458,6 +1554,16 @@ supported_plots <- function() {
|
|||
tertiary.type = c("dichotomous", "ordinal"),
|
||||
secondary.extra = NULL
|
||||
),
|
||||
plot_box = list(
|
||||
fun = "plot_box",
|
||||
descr = "Box plot",
|
||||
note = "A classic way to plot data distribution by groups",
|
||||
primary.type = c("continuous", "dichotomous", "ordinal"),
|
||||
secondary.type = c("dichotomous", "ordinal"),
|
||||
secondary.multi = FALSE,
|
||||
tertiary.type = c("dichotomous", "ordinal"),
|
||||
secondary.extra = "none"
|
||||
),
|
||||
plot_euler = list(
|
||||
fun = "plot_euler",
|
||||
descr = "Euler diagram",
|
||||
|
|
@ -1629,18 +1735,49 @@ line_break <- function(data, lineLength = 20, fixed = FALSE) {
|
|||
}
|
||||
|
||||
|
||||
wrap_plot_list <- function(data) {
|
||||
if (length(data) > 1) {
|
||||
out <- data |>
|
||||
allign_axes() |>
|
||||
patchwork::wrap_plots(guides = "collect", axes = "collect", axis_titles = "collect")
|
||||
#' Wrapping
|
||||
#'
|
||||
#' @param data list of ggplot2 objects
|
||||
#' @param tag_levels passed to patchwork::plot_annotation if given. Default is NULL
|
||||
#'
|
||||
#' @returns list of ggplot2 objects
|
||||
#' @export
|
||||
#'
|
||||
wrap_plot_list <- function(data, tag_levels = NULL) {
|
||||
if (ggplot2::is.ggplot(data[[1]])) {
|
||||
if (length(data) > 1) {
|
||||
out <- data |>
|
||||
(\(.x){
|
||||
if (rlang::is_named(.x)) {
|
||||
purrr::imap(.x, \(.y, .i){
|
||||
.y + ggplot2::ggtitle(.i)
|
||||
})
|
||||
} else {
|
||||
.x
|
||||
}
|
||||
})() |>
|
||||
allign_axes() |>
|
||||
patchwork::wrap_plots(guides = "collect", axes = "collect", axis_titles = "collect")
|
||||
if (!is.null(tag_levels)) {
|
||||
out <- out + patchwork::plot_annotation(tag_levels = tag_levels)
|
||||
}
|
||||
} else {
|
||||
out <- data
|
||||
}
|
||||
} else {
|
||||
out <- data
|
||||
cli::cli_abort("Can only wrap lists of {.cls ggplot} objects")
|
||||
}
|
||||
out
|
||||
}
|
||||
|
||||
|
||||
#' Alligns axes between plots
|
||||
#'
|
||||
#' @param ... ggplot2 objects or list of ggplot2 objects
|
||||
#'
|
||||
#' @returns list of ggplot2 objects
|
||||
#' @export
|
||||
#'
|
||||
allign_axes <- function(...) {
|
||||
# https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object
|
||||
# https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150
|
||||
|
|
@ -1652,20 +1789,34 @@ allign_axes <- function(...) {
|
|||
cli::cli_abort("Can only align {.cls ggplot} objects or a list of them")
|
||||
}
|
||||
|
||||
# browser()
|
||||
yr <- purrr::map(p, ~ ggplot2::layer_scales(.x)$y$get_limits()) |>
|
||||
unlist() |>
|
||||
range() |>
|
||||
unique()
|
||||
yr <- clean_common_axis(p, "y")
|
||||
|
||||
xr <- purrr::map(p, ~ ggplot2::layer_scales(.x)$x$get_limits()) |>
|
||||
unlist() |>
|
||||
range() |>
|
||||
unique()
|
||||
xr <- clean_common_axis(p, "x")
|
||||
|
||||
p |> purrr::map(~ .x + ggplot2::xlim(xr) + ggplot2::ylim(yr))
|
||||
}
|
||||
|
||||
#' Extract and clean axis ranges
|
||||
#'
|
||||
#' @param p plot
|
||||
#' @param axis axis. x or y.
|
||||
#'
|
||||
#' @returns vector
|
||||
#' @export
|
||||
#'
|
||||
clean_common_axis <- function(p, axis) {
|
||||
purrr::map(p, ~ ggplot2::layer_scales(.x)[[axis]]$get_limits()) |>
|
||||
unlist() |>
|
||||
(\(.x){
|
||||
if (is.numeric(.x)) {
|
||||
range(.x)
|
||||
} else {
|
||||
.x
|
||||
}
|
||||
})() |>
|
||||
unique()
|
||||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: R//data-import.R
|
||||
|
|
@ -1732,27 +1883,7 @@ data_import_server <- function(id) {
|
|||
id = ns("file_import"),
|
||||
show_data_in = "popup",
|
||||
trigger_return = "change",
|
||||
return_class = "data.frame",
|
||||
read_fns = list(
|
||||
ods = import_ods,
|
||||
dta = function(file) {
|
||||
haven::read_dta(
|
||||
file = file,
|
||||
.name_repair = "unique_quiet"
|
||||
)
|
||||
},
|
||||
csv = import_delim,
|
||||
tsv = import_delim,
|
||||
txt = import_delim,
|
||||
xls = import_xls,
|
||||
xlsx = import_xls,
|
||||
rds = function(file) {
|
||||
readr::read_rds(
|
||||
file = file,
|
||||
name_repair = "unique_quiet"
|
||||
)
|
||||
}
|
||||
)
|
||||
return_class = "data.frame"
|
||||
)
|
||||
|
||||
shiny::observeEvent(data_file$data(), {
|
||||
|
|
@ -2505,7 +2636,9 @@ default_parsing <- function(data) {
|
|||
out <- data |>
|
||||
REDCapCAST::parse_data() |>
|
||||
REDCapCAST::as_factor() |>
|
||||
REDCapCAST::numchar2fct()
|
||||
REDCapCAST::numchar2fct(numeric.threshold = 8,character.throshold = 10) |>
|
||||
REDCapCAST::as_logical() |>
|
||||
REDCapCAST::fct_drop()
|
||||
|
||||
purrr::map2(out,name_labels,\(.x,.l){
|
||||
if (!(is.na(.l) | .l=="")) {
|
||||
|
|
@ -2565,6 +2698,7 @@ remove_empty_cols <- function(data,cutoff=.7){
|
|||
#' @param index index name
|
||||
#'
|
||||
#' @returns list
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' ls_d <- list(test=c(1:20))
|
||||
|
|
@ -2858,7 +2992,7 @@ import_file_server <- function(id,
|
|||
parameters <- parameters[which(names(parameters) %in% rlang::fn_fmls_names(get(read_fns[[extension]])))]
|
||||
# parameters <- parameters[which(names(parameters) %in% rlang::fn_fmls_names(read_fns[[extension]]))]
|
||||
imported <- try(rlang::exec(read_fns[[extension]], !!!parameters), silent = TRUE)
|
||||
code <- rlang::call2(read_fns[[extension]], !!!modifyList(parameters, list(file = input$file$name)), .ns = "freesearcheR")
|
||||
code <- rlang::call2(read_fns[[extension]], !!!modifyList(parameters, list(file = input$file$name)), .ns = "FreesearchR")
|
||||
|
||||
if (inherits(imported, "try-error")) {
|
||||
imported <- try(rlang::exec(rio::import, !!!parameters[1]), silent = TRUE)
|
||||
|
|
@ -3173,6 +3307,117 @@ import_file_demo_app <- function() {
|
|||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: R//launch_FreesearchR.R
|
||||
########
|
||||
|
||||
#' Easily launch the FreesearchR app
|
||||
#'
|
||||
#' @description
|
||||
#' All data.frames in the global environment will be accessible through the app.
|
||||
#'
|
||||
#' @param ... passed on to `shiny::runApp()`
|
||||
#'
|
||||
#' @returns shiny app
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' \dontrun{
|
||||
#' data(mtcars)
|
||||
#' shiny_FreesearchR(launch.browser = TRUE)
|
||||
#' }
|
||||
launch_FreesearchR <- function(...){
|
||||
appDir <- system.file("apps", "FreesearchR", package = "FreesearchR")
|
||||
if (appDir == "") {
|
||||
stop("Could not find the app directory. Try re-installing `FreesearchR`.", call. = FALSE)
|
||||
}
|
||||
|
||||
a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...)
|
||||
return(invisible(a))
|
||||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: R//plot_box.R
|
||||
########
|
||||
|
||||
#' Beautiful box plot(s)
|
||||
#'
|
||||
#' @returns ggplot2 object
|
||||
#' @export
|
||||
#'
|
||||
#' @name data-plots
|
||||
#'
|
||||
#' @examples
|
||||
#' mtcars |> plot_box(x = "mpg", y = "cyl", z = "gear")
|
||||
#' mtcars |>
|
||||
#' default_parsing() |>
|
||||
#' plot_box(x = "mpg", y = "cyl", z = "gear")
|
||||
plot_box <- function(data, x, y, z = NULL) {
|
||||
if (!is.null(z)) {
|
||||
ds <- split(data, data[z])
|
||||
} else {
|
||||
ds <- list(data)
|
||||
}
|
||||
|
||||
out <- lapply(ds, \(.ds){
|
||||
plot_box_single(
|
||||
data = .ds,
|
||||
x = x,
|
||||
y = y
|
||||
)
|
||||
})
|
||||
|
||||
wrap_plot_list(out)
|
||||
# patchwork::wrap_plots(out,guides = "collect")
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
#' Create nice box-plots
|
||||
#'
|
||||
#' @name data-plots
|
||||
#'
|
||||
#' @returns
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' mtcars |> plot_box_single("mpg","cyl")
|
||||
plot_box_single <- function(data, x, y=NULL, seed = 2103) {
|
||||
set.seed(seed)
|
||||
|
||||
if (is.null(y)) {
|
||||
y <- "All"
|
||||
data[[y]] <- y
|
||||
}
|
||||
|
||||
discrete <- !outcome_type(data[[y]]) %in% "continuous"
|
||||
|
||||
data |>
|
||||
ggplot2::ggplot(ggplot2::aes(x = !!dplyr::sym(x), y = !!dplyr::sym(y), fill = !!dplyr::sym(y), group = !!dplyr::sym(y))) +
|
||||
ggplot2::geom_boxplot(linewidth = 1.8, outliers = FALSE) +
|
||||
## THis could be optional in future
|
||||
ggplot2::geom_jitter(color = "black", size = 2, alpha = 0.9) +
|
||||
ggplot2::coord_flip() +
|
||||
# viridis::scale_fill_viridis(discrete = discrete, option = "C") +
|
||||
# ggplot2::theme_void() +
|
||||
ggplot2::theme(
|
||||
legend.position = "none",
|
||||
# panel.grid.major = element_blank(),
|
||||
# panel.grid.minor = element_blank(),
|
||||
# axis.text.y = element_blank(),
|
||||
# axis.title.y = element_blank(),
|
||||
text = ggplot2::element_text(size = 20),
|
||||
# axis.text = ggplot2::element_blank(),
|
||||
# plot.title = element_blank(),
|
||||
panel.background = ggplot2::element_rect(fill = "white"),
|
||||
plot.background = ggplot2::element_rect(fill = "white"),
|
||||
panel.border = ggplot2::element_blank()
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: R//plot_euler.R
|
||||
########
|
||||
|
|
@ -3257,9 +3502,6 @@ ggeulerr <- function(
|
|||
#' mtcars |> plot_euler("vs", "am", seed = 1)
|
||||
plot_euler <- function(data, x, y, z = NULL, seed = 2103) {
|
||||
set.seed(seed = seed)
|
||||
|
||||
# data <- data[c(...,z)]
|
||||
|
||||
if (!is.null(z)) {
|
||||
ds <- split(data, data[z])
|
||||
} else {
|
||||
|
|
@ -3272,6 +3514,7 @@ plot_euler <- function(data, x, y, z = NULL, seed = 2103) {
|
|||
plot_euler_single()
|
||||
})
|
||||
|
||||
# names(out)
|
||||
wrap_plot_list(out)
|
||||
# patchwork::wrap_plots(out, guides = "collect")
|
||||
}
|
||||
|
|
@ -3295,7 +3538,7 @@ plot_euler_single <- function(data) {
|
|||
ggeulerr(shape = "circle") +
|
||||
ggplot2::theme_void() +
|
||||
ggplot2::theme(
|
||||
legend.position = "right",
|
||||
legend.position = "none",
|
||||
# panel.grid.major = element_blank(),
|
||||
# panel.grid.minor = element_blank(),
|
||||
# axis.text.y = element_blank(),
|
||||
|
|
@ -4972,15 +5215,16 @@ regression_model_uv_list <- function(data,
|
|||
#'
|
||||
#' @examples
|
||||
#' \dontrun{
|
||||
#' mod <- lm(mpg ~ ., mtcars)
|
||||
#' mod <- lm(mpg ~ ., default_parsing(mtcars))
|
||||
#' p <- mod |>
|
||||
#' gtsummary::tbl_regression() |>
|
||||
#' plot(colour = "variable")
|
||||
#' }
|
||||
#'
|
||||
plot.tbl_regression <- function(x,
|
||||
# remove_header_rows = TRUE,
|
||||
# remove_reference_rows = FALSE,
|
||||
plot_ref = TRUE,
|
||||
remove_header_rows = TRUE,
|
||||
remove_reference_rows = FALSE,
|
||||
...) {
|
||||
# check_dots_empty()
|
||||
gtsummary:::check_pkg_installed("ggstats")
|
||||
|
|
@ -4989,33 +5233,31 @@ plot.tbl_regression <- function(x,
|
|||
# gtsummary:::check_scalar_logical(remove_reference_rows)
|
||||
|
||||
df_coefs <- x$table_body
|
||||
# if (isTRUE(remove_header_rows)) {
|
||||
# df_coefs <- df_coefs |> dplyr::filter(!.data$header_row %in% TRUE)
|
||||
# }
|
||||
# if (isTRUE(remove_reference_rows)) {
|
||||
# df_coefs <- df_coefs |> dplyr::filter(!.data$reference_row %in% TRUE)
|
||||
# }
|
||||
|
||||
# browser()
|
||||
if (isTRUE(remove_header_rows)) {
|
||||
df_coefs <- df_coefs |> dplyr::filter(!header_row %in% TRUE)
|
||||
}
|
||||
if (isTRUE(remove_reference_rows)) {
|
||||
df_coefs <- df_coefs |> dplyr::filter(!reference_row %in% TRUE)
|
||||
}
|
||||
|
||||
# Removes redundant label
|
||||
df_coefs$label[df_coefs$row_type == "label"] <- ""
|
||||
|
||||
df_coefs %>%
|
||||
# Add estimate value to reference level
|
||||
if (plot_ref == TRUE){
|
||||
df_coefs[df_coefs$var_type == "categorical" & is.na(df_coefs$reference_row),"estimate"] <- if (x$inputs$exponentiate) 1 else 0}
|
||||
|
||||
p <- df_coefs |>
|
||||
ggstats::ggcoef_plot(exponentiate = x$inputs$exponentiate, ...)
|
||||
|
||||
if (x$inputs$exponentiate){
|
||||
p <- symmetrical_scale_x_log10(p)
|
||||
}
|
||||
p
|
||||
}
|
||||
|
||||
|
||||
# default_parsing(mtcars) |> lapply(class)
|
||||
#
|
||||
# purrr::imap(mtcars,\(.x,.i){
|
||||
# if (.i %in% c("vs","am","gear","carb")){
|
||||
# as.factor(.x)
|
||||
# } else .x
|
||||
# }) |> dplyr::bind_cols()
|
||||
#
|
||||
#
|
||||
|
||||
|
||||
#' Wrapper to pivot gtsummary table data to long for plotting
|
||||
#'
|
||||
#' @param list a custom regression models list
|
||||
|
|
@ -5057,6 +5299,50 @@ merge_long <- function(list, model.names) {
|
|||
}
|
||||
|
||||
|
||||
#' Easily round log scale limits for nice plots
|
||||
#'
|
||||
#' @param data data
|
||||
#' @param fun rounding function (floor/ceiling)
|
||||
#' @param ... ignored
|
||||
#'
|
||||
#' @returns numeric vector
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' limit_log(-.1,floor)
|
||||
#' limit_log(.1,ceiling)
|
||||
#' limit_log(-2.1,ceiling)
|
||||
#' limit_log(2.1,ceiling)
|
||||
limit_log <- function(data,fun,...){
|
||||
fun(10^-floor(data)*10^data)/10^-floor(data)
|
||||
}
|
||||
|
||||
#' Ensure symmetrical plot around 1 on a logarithmic x scale for ratio plots
|
||||
#'
|
||||
#' @param plot ggplot2 plot
|
||||
#' @param breaks breaks used and mirrored
|
||||
#' @param ... ignored
|
||||
#'
|
||||
#' @returns ggplot2 object
|
||||
#' @export
|
||||
#'
|
||||
symmetrical_scale_x_log10 <- function(plot,breaks=c(1,2,3,5,10),...){
|
||||
rx <- ggplot2::layer_scales(plot)$x$get_limits()
|
||||
|
||||
x_min <- floor(10*rx[1])/10
|
||||
x_max <- ceiling(10*rx[2])/10
|
||||
|
||||
rx_min <- limit_log(rx[1],floor)
|
||||
rx_max <- limit_log(rx[2],ceiling)
|
||||
|
||||
max_abs_x <- max(abs(c(x_min,x_max)))
|
||||
|
||||
ticks <- log10(breaks)+(ceiling(max_abs_x)-1)
|
||||
browser()
|
||||
plot + ggplot2::scale_x_log10(limits=c(rx_min,rx_max),breaks=create_log_tics(10^ticks[ticks<=max_abs_x]))
|
||||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: R//regression_table.R
|
||||
########
|
||||
|
|
@ -5144,7 +5430,7 @@ merge_long <- function(list, model.names) {
|
|||
#' #' @export
|
||||
#' regression_table.default <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
|
||||
#' # Stripping custom class
|
||||
#' class(x) <- class(x)[class(x) != "freesearcher_model"]
|
||||
#' class(x) <- class(x)[class(x) != "freesearchr_model"]
|
||||
#'
|
||||
#' if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
|
||||
#' if (!"exponentiate" %in% names(args.list)) {
|
||||
|
|
@ -5173,7 +5459,7 @@ regression_table <- function(x, ...) {
|
|||
|
||||
regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
|
||||
# Stripping custom class
|
||||
class(x) <- class(x)[class(x) != "freesearcher_model"]
|
||||
class(x) <- class(x)[class(x) != "freesearchr_model"]
|
||||
|
||||
if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
|
||||
if (!"exponentiate" %in% names(args.list)) {
|
||||
|
|
@ -5296,49 +5582,6 @@ modify_qmd <- function(file, format) {
|
|||
|
||||
|
||||
|
||||
########
|
||||
#### Current file: R//shiny_freesearcheR.R
|
||||
########
|
||||
|
||||
#' Launch the freesearcheR tool locally
|
||||
#'
|
||||
#' @description
|
||||
#' All data.frames in the global environment will be accessible through the app.
|
||||
#'
|
||||
#'
|
||||
#' @param ... arguments passed on to `shiny::runApp()`
|
||||
#'
|
||||
#' @return shiny app
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' \dontrun{
|
||||
#' data(mtcars)
|
||||
#' shiny_freesearcheR(launch.browser = TRUE)
|
||||
#' }
|
||||
shiny_freesearcheR <- function(...) {
|
||||
appDir <- system.file("apps", "freesearcheR", package = "freesearcheR")
|
||||
if (appDir == "") {
|
||||
stop("Could not find the app directory. Try re-installing `freesearcheR`.", call. = FALSE)
|
||||
}
|
||||
|
||||
a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...)
|
||||
return(invisible(a))
|
||||
}
|
||||
|
||||
|
||||
#' Easily launch the freesearcheR app
|
||||
#'
|
||||
#' @param ... passed on to `shiny::runApp()`
|
||||
#'
|
||||
#' @returns shiny app
|
||||
#' @export
|
||||
#'
|
||||
launch_freesearcheR <- function(...){
|
||||
shiny_freesearcheR(...)
|
||||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: R//theme.R
|
||||
########
|
||||
|
|
@ -5692,7 +5935,7 @@ modal_update_factor <- function(id,
|
|||
#'
|
||||
#' @importFrom shinyWidgets WinBox wbOptions wbControls
|
||||
#' @importFrom htmltools tagList
|
||||
#' @rdname create-column
|
||||
#' @rdname update-factor
|
||||
winbox_update_factor <- function(id,
|
||||
title = i18n("Update levels of a factor"),
|
||||
options = shinyWidgets::wbOptions(),
|
||||
|
|
@ -6660,7 +6903,7 @@ grepl_fix <- function(data, pattern, type = c("prefix", "infix", "suffix")) {
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/freesearcheR/ui.R
|
||||
#### Current file: /Users/au301842/FreesearchR/inst/apps/FreesearchR/ui.R
|
||||
########
|
||||
|
||||
# ns <- NS(id)
|
||||
|
|
@ -6672,7 +6915,7 @@ ui_elements <- list(
|
|||
#########
|
||||
##############################################################################
|
||||
"home" = bslib::nav_panel(
|
||||
title = "freesearcheR",
|
||||
title = "FreesearchR",
|
||||
shiny::fluidRow(
|
||||
shiny::column(width = 2),
|
||||
shiny::column(
|
||||
|
|
@ -7263,10 +7506,10 @@ ui <- bslib::page_fixed(
|
|||
# add the name of the tab you want to use as title in data-value
|
||||
shiny::HTML(
|
||||
".container-fluid > .nav > li >
|
||||
a[data-value='freesearcheR'] {font-size: 28px}"
|
||||
a[data-value='FreesearchR'] {font-size: 28px}"
|
||||
)
|
||||
),
|
||||
title = "freesearcheR",
|
||||
title = "FreesearchR",
|
||||
theme = light,
|
||||
shiny::useBusyIndicators(),
|
||||
bslib::page_navbar(
|
||||
|
|
@ -7289,7 +7532,7 @@ ui <- bslib::page_fixed(
|
|||
),
|
||||
shiny::p(
|
||||
style = "margin: 1; color: #888;",
|
||||
"AG Damsbo | v", app_version(), " | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer")
|
||||
"AG Damsbo | v", app_version(), " | ",shiny::tags$a("AGPLv3 license", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer")," | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer")
|
||||
),
|
||||
)
|
||||
)
|
||||
|
|
@ -7297,7 +7540,7 @@ ui <- bslib::page_fixed(
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/freesearcheR/server.R
|
||||
#### Current file: /Users/au301842/FreesearchR/inst/apps/FreesearchR/server.R
|
||||
########
|
||||
|
||||
library(readr)
|
||||
|
|
@ -7328,7 +7571,7 @@ library(IDEAFilter)
|
|||
library(shinyWidgets)
|
||||
library(DT)
|
||||
library(gtsummary)
|
||||
# library(freesearcheR)
|
||||
# library(FreesearchR)
|
||||
|
||||
# source("functions.R")
|
||||
|
||||
|
|
@ -7476,7 +7719,7 @@ server <- function(input, output, session) {
|
|||
paste(collapse = "") |>
|
||||
paste("|>
|
||||
dplyr::select(", paste(input$import_var, collapse = ","), ") |>
|
||||
freesearcheR::default_parsing()") |>
|
||||
FreesearchR::default_parsing()") |>
|
||||
(\(.x){
|
||||
paste0("data <- ", .x)
|
||||
})()
|
||||
|
|
@ -8279,7 +8522,7 @@ server <- function(input, output, session) {
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/freesearcheR/launch.R
|
||||
#### Current file: /Users/au301842/FreesearchR/inst/apps/FreesearchR/launch.R
|
||||
########
|
||||
|
||||
shinyApp(ui, server)
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ library(IDEAFilter)
|
|||
library(shinyWidgets)
|
||||
library(DT)
|
||||
library(gtsummary)
|
||||
# library(freesearcheR)
|
||||
# library(FreesearchR)
|
||||
|
||||
# source("functions.R")
|
||||
|
||||
|
|
@ -174,7 +174,7 @@ server <- function(input, output, session) {
|
|||
paste(collapse = "") |>
|
||||
paste("|>
|
||||
dplyr::select(", paste(input$import_var, collapse = ","), ") |>
|
||||
freesearcheR::default_parsing()") |>
|
||||
FreesearchR::default_parsing()") |>
|
||||
(\(.x){
|
||||
paste0("data <- ", .x)
|
||||
})()
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ ui_elements <- list(
|
|||
#########
|
||||
##############################################################################
|
||||
"home" = bslib::nav_panel(
|
||||
title = "freesearcheR",
|
||||
title = "FreesearchR",
|
||||
shiny::fluidRow(
|
||||
shiny::column(width = 2),
|
||||
shiny::column(
|
||||
|
|
@ -598,10 +598,10 @@ ui <- bslib::page_fixed(
|
|||
# add the name of the tab you want to use as title in data-value
|
||||
shiny::HTML(
|
||||
".container-fluid > .nav > li >
|
||||
a[data-value='freesearcheR'] {font-size: 28px}"
|
||||
a[data-value='FreesearchR'] {font-size: 28px}"
|
||||
)
|
||||
),
|
||||
title = "freesearcheR",
|
||||
title = "FreesearchR",
|
||||
theme = light,
|
||||
shiny::useBusyIndicators(),
|
||||
bslib::page_navbar(
|
||||
|
|
@ -624,7 +624,7 @@ ui <- bslib::page_fixed(
|
|||
),
|
||||
shiny::p(
|
||||
style = "margin: 1; color: #888;",
|
||||
"AG Damsbo | v", app_version(), " | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer")
|
||||
"AG Damsbo | v", app_version(), " | ",shiny::tags$a("AGPLv3 license", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer")," | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer")
|
||||
),
|
||||
)
|
||||
)
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
# Welcome
|
||||
|
||||
This is the ***freesearcheR*** data analysis tool. We intend the ***freesearcheR*** to be a powerful and free tool for easy data evaluation and analysis at the hands of the clinician. If you need more advanced tools for regression models or plotting, you'll probably be better off using *R* or similar directly on your own machine.
|
||||
This is the ***FreesearchR*** data analysis tool. We intend the ***FreesearchR*** to be a powerful and free tool for easy data evaluation and analysis at the hands of the clinician. If you need more advanced tools for regression models or plotting, you'll probably be better off using *R* or similar directly on your own machine.
|
||||
|
||||
By intention, this tool has been designed to be simple to use with a minimum of mandatory options to keep the workflow streamlined, while also including a few options to go even further.
|
||||
|
||||
|
|
@ -24,6 +24,6 @@ There are some simple steps to go through (see corresponding tabs in the top):
|
|||
|
||||
1. Export the the analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) as well as the data with preserved metadata.
|
||||
|
||||
Have a look at the [documentations page](https://agdamsbo.github.io/freesearcheR/) for further project description. If you're interested in the source code, then go on, [have a look](https://github.com/agdamsbo/freesearcheR)!
|
||||
The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) for documenting the project, functions, road map and more. If you're interested in the source code, then [everything is open and you are free to read, copy, modify and improve](https://github.com/agdamsbo/FreesearchR), and please let us know if you want to contribute!
|
||||
|
||||
If you encounter anything strange or the app doesn't act as expected. Please [report on Github](https://github.com/agdamsbo/freesearcheR/issues).
|
||||
Contributions can be reporting issues, suggesting new functionality, improving code or any other feedback. [It all goes here](https://github.com/agdamsbo/FreesearchR/issues).
|
||||
|
|
|
|||
17
man/allign_axes.Rd
Normal file
17
man/allign_axes.Rd
Normal file
|
|
@ -0,0 +1,17 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/data_plots.R
|
||||
\name{allign_axes}
|
||||
\alias{allign_axes}
|
||||
\title{Alligns axes between plots}
|
||||
\usage{
|
||||
allign_axes(...)
|
||||
}
|
||||
\arguments{
|
||||
\item{...}{ggplot2 objects or list of ggplot2 objects}
|
||||
}
|
||||
\value{
|
||||
list of ggplot2 objects
|
||||
}
|
||||
\description{
|
||||
Alligns axes between plots
|
||||
}
|
||||
27
man/limit_log.Rd
Normal file
27
man/limit_log.Rd
Normal file
|
|
@ -0,0 +1,27 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/regression_plot.R
|
||||
\name{limit_log}
|
||||
\alias{limit_log}
|
||||
\title{Easily round log scale limits for nice plots}
|
||||
\usage{
|
||||
limit_log(data, fun, ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{data}{data}
|
||||
|
||||
\item{fun}{rounding function (floor/ceiling)}
|
||||
|
||||
\item{...}{ignored}
|
||||
}
|
||||
\value{
|
||||
numeric vector
|
||||
}
|
||||
\description{
|
||||
Easily round log scale limits for nice plots
|
||||
}
|
||||
\examples{
|
||||
limit_log(-.1,floor)
|
||||
limit_log(.1,ceiling)
|
||||
limit_log(-2.1,ceiling)
|
||||
limit_log(2.1,ceiling)
|
||||
}
|
||||
21
man/symmetrical_scale_x_log10.Rd
Normal file
21
man/symmetrical_scale_x_log10.Rd
Normal file
|
|
@ -0,0 +1,21 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/regression_plot.R
|
||||
\name{symmetrical_scale_x_log10}
|
||||
\alias{symmetrical_scale_x_log10}
|
||||
\title{Ensure symmetrical plot around 1 on a logarithmic x scale for ratio plots}
|
||||
\usage{
|
||||
symmetrical_scale_x_log10(plot, breaks = c(1, 2, 3, 5, 10), ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{plot}{ggplot2 plot}
|
||||
|
||||
\item{breaks}{breaks used and mirrored}
|
||||
|
||||
\item{...}{ignored}
|
||||
}
|
||||
\value{
|
||||
ggplot2 object
|
||||
}
|
||||
\description{
|
||||
Ensure symmetrical plot around 1 on a logarithmic x scale for ratio plots
|
||||
}
|
||||
19
man/wrap_plot_list.Rd
Normal file
19
man/wrap_plot_list.Rd
Normal file
|
|
@ -0,0 +1,19 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/data_plots.R
|
||||
\name{wrap_plot_list}
|
||||
\alias{wrap_plot_list}
|
||||
\title{Wrapping}
|
||||
\usage{
|
||||
wrap_plot_list(data, tag_levels = NULL)
|
||||
}
|
||||
\arguments{
|
||||
\item{data}{list of ggplot2 objects}
|
||||
|
||||
\item{tag_levels}{passed to patchwork::plot_annotation if given. Default is NULL}
|
||||
}
|
||||
\value{
|
||||
list of ggplot2 objects
|
||||
}
|
||||
\description{
|
||||
Wrapping
|
||||
}
|
||||
89
renv.lock
89
renv.lock
File diff suppressed because one or more lines are too long
|
|
@ -2,7 +2,7 @@
|
|||
local({
|
||||
|
||||
# the requested version of renv
|
||||
version <- "1.1.2"
|
||||
version <- "1.1.3"
|
||||
attr(version, "sha") <- NULL
|
||||
|
||||
# the project directory
|
||||
|
|
@ -695,11 +695,19 @@ local({
|
|||
|
||||
}
|
||||
|
||||
renv_bootstrap_platform_prefix <- function() {
|
||||
renv_bootstrap_platform_prefix_default <- function() {
|
||||
|
||||
# construct version prefix
|
||||
version <- paste(R.version$major, R.version$minor, sep = ".")
|
||||
prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
|
||||
# read version component
|
||||
version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v")
|
||||
|
||||
# expand placeholders
|
||||
placeholders <- list(
|
||||
list("%v", format(getRversion()[1, 1:2])),
|
||||
list("%V", format(getRversion()[1, 1:3]))
|
||||
)
|
||||
|
||||
for (placeholder in placeholders)
|
||||
version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE)
|
||||
|
||||
# include SVN revision for development versions of R
|
||||
# (to avoid sharing platform-specific artefacts with released versions of R)
|
||||
|
|
@ -708,10 +716,19 @@ local({
|
|||
identical(R.version[["nickname"]], "Unsuffered Consequences")
|
||||
|
||||
if (devel)
|
||||
prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
|
||||
version <- paste(version, R.version[["svn rev"]], sep = "-r")
|
||||
|
||||
version
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_platform_prefix <- function() {
|
||||
|
||||
# construct version prefix
|
||||
version <- renv_bootstrap_platform_prefix_default()
|
||||
|
||||
# build list of path components
|
||||
components <- c(prefix, R.version$platform)
|
||||
components <- c(version, R.version$platform)
|
||||
|
||||
# include prefix if provided by user
|
||||
prefix <- renv_bootstrap_platform_prefix_impl()
|
||||
|
|
@ -1202,15 +1219,18 @@ local({
|
|||
list(
|
||||
|
||||
# objects
|
||||
list("{", "\t\n\tobject(\t\n\t"),
|
||||
list("}", "\t\n\t)\t\n\t"),
|
||||
list("{", "\t\n\tobject(\t\n\t", TRUE),
|
||||
list("}", "\t\n\t)\t\n\t", TRUE),
|
||||
|
||||
# arrays
|
||||
list("[", "\t\n\tarray(\t\n\t"),
|
||||
list("]", "\n\t\n)\n\t\n"),
|
||||
list("[", "\t\n\tarray(\t\n\t", TRUE),
|
||||
list("]", "\n\t\n)\n\t\n", TRUE),
|
||||
|
||||
# maps
|
||||
list(":", "\t\n\t=\t\n\t")
|
||||
list(":", "\t\n\t=\t\n\t", TRUE),
|
||||
|
||||
# newlines
|
||||
list("\\u000a", "\n", FALSE)
|
||||
|
||||
)
|
||||
|
||||
|
|
@ -1287,7 +1307,8 @@ local({
|
|||
# evaluate in safe environment
|
||||
result <- eval(json, envir = renv_json_read_envir())
|
||||
|
||||
# fix up strings if necessary
|
||||
# fix up strings if necessary -- do so only with reversible patterns
|
||||
patterns <- Filter(function(pattern) pattern[[3L]], patterns)
|
||||
renv_json_read_remap(result, patterns)
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue