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averissimoaverissimo
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Merge branch 'main' into 899-report_missing_data
2 parents b6827bc + 29f33ff commit f71de82

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‎.pre-commit-config.yaml‎

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@@ -6,7 +6,7 @@ default_language_version:
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python: python3
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repos:
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- repo: https://github.com/lorenzwalthert/precommit
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rev: v0.4.3.9012
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rev: v0.4.3.9013
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hooks:
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- id: style-files
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name: Style code with `styler`

‎DESCRIPTION‎

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@@ -1,8 +1,8 @@
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Type: Package
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Package: teal.modules.general
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Title: General Modules for 'teal' Applications
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Version: 0.4.1.9012
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Date: 2025-07-24
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Version: 0.4.1.9014
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Date: 2025-08-04
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Authors@R: c(
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person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
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person("Pawel", "Rucki", , "[email protected]", role = "aut"),
@@ -26,7 +26,7 @@ Depends:
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ggmosaic (>= 0.3.0),
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ggplot2 (>= 3.4.0),
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R (>= 4.1),
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shiny (>= 1.6.0),
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shiny (>= 1.8.1),
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teal (>= 0.16.0.9008),
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teal.transform (>= 0.6.0.9002)
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Imports:

‎NEWS.md‎

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@@ -1,4 +1,4 @@
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# teal.modules.general 0.4.1.9012
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# teal.modules.general 0.4.1.9014
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### Bug fixes
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‎R/tm_a_pca.R‎

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@@ -229,7 +229,6 @@ ui_a_pca <- function(id, ...) {
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}
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tagList(
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include_css_files("custom"),
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teal.widgets::standard_layout(
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output = teal.widgets::white_small_well(
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uiOutput(ns("all_plots"))

‎R/tm_data_table.R‎

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@@ -158,7 +158,6 @@ ui_page_data_table <- function(id, pre_output = NULL, post_output = NULL) {
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ns <- NS(id)
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tagList(
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include_css_files("custom"),
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teal.widgets::standard_layout(
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output = teal.widgets::white_small_well(
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bslib::page_fluid(

‎R/tm_file_viewer.R‎

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Original file line numberDiff line numberDiff line change
@@ -103,13 +103,12 @@ ui_viewer <- function(id, ...) {
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ns <- NS(id)
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tagList(
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include_css_files("custom"),
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teal.widgets::standard_layout(
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output = tags$div(
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uiOutput(ns("output"))
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),
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encoding = tags$div(
112-
class = "file_viewer_encoding",
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style = "overflow-y: hidden; overflow-x: auto;",
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tags$label("Encodings", class = "text-primary"),
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shinyTree::shinyTree(
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ns("tree"),
@@ -173,7 +172,7 @@ srv_viewer <- function(id, input_path) {
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tags$img(src = con_type$selected_path, alt = "file does not exist")
174173
} else if (file_extension == "pdf") {
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tags$embed(
176-
class = "embed_pdf",
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style = "height: 600px; width: 100%;",
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src = con_type$selected_path
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)
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} else if (!isFALSE(con_type$output_text[1])) {

‎R/tm_front_page.R‎

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Original file line numberDiff line numberDiff line change
@@ -119,33 +119,32 @@ ui_front_page <- function(id, ...) {
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ns <- NS(id)
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tagList(
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include_css_files("custom"),
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tags$div(
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id = "front_page_content",
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class = "ml-8",
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style = "margin-left: 2rem;",
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tags$div(
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id = "front_page_headers",
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get_header_tags(args$header_text)
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),
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tags$div(
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id = "front_page_tables",
132-
class = "ml-4",
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style = "margin-left: 2rem;",
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get_table_tags(args$tables, ns)
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),
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tags$div(
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id = "front_page_custom_html",
137-
class = "my-4",
136+
style = "margin-left: 2rem;",
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args$additional_tags
139138
),
140139
if (length(args$datanames) > 0L) {
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tags$div(
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id = "front_page_metabutton",
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class = "m-4",
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style = "margin: 1rem;",
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actionButton(ns("metadata_button"), "Show metadata")
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)
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},
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tags$footer(
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class = ".small",
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class = "small",
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get_footer_tags(args$footnotes)
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)
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)
@@ -228,7 +227,7 @@ get_table_tags <- function(tables, ns) {
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tableOutput(ns(paste0("table_", idx)))
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)
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}))
231-
return(table_tags)
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table_tags
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}
233232

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get_footer_tags <- function(footnotes) {
@@ -255,11 +254,11 @@ convert_metadata_to_dataframe <- function(raw_metadata, datanames) {
255254
if (is.null(metadata)) {
256255
return(data.frame(Dataset = character(0), Name = character(0), Value = character(0)))
257256
}
258-
return(data.frame(
257+
data.frame(
259258
Dataset = dataname,
260259
Name = names(metadata),
261260
Value = unname(unlist(lapply(metadata, as.character)))
262-
))
261+
)
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}, raw_metadata, datanames, SIMPLIFY = FALSE)
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do.call(rbind, output)
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}

‎R/tm_g_scatterplot.R‎

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@@ -362,11 +362,11 @@ ui_g_scatterplot <- function(id, ...) {
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)
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tagList(
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include_css_files("custom"),
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teal.widgets::standard_layout(
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output = teal.widgets::white_small_well(
368367
teal.widgets::plot_with_settings_ui(id = ns("scatter_plot")),
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tags$h1(tags$strong("Selected points:"), class = "text-center font-150p"),
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tags$br(),
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tags$h1(tags$strong("Selected points:"), style = "font-size: 150%;"),
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teal.widgets::get_dt_rows(ns("data_table"), ns("data_table_rows")),
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DT::dataTableOutput(ns("data_table"), width = "100%")
372372
),
@@ -470,16 +470,16 @@ ui_g_scatterplot <- function(id, ...) {
470470
tags$div(
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id = ns("label_pos"),
472472
tags$div(tags$strong("Stats position")),
473-
tags$div(class = "inline-block w-10", helpText("Left")),
473+
tags$div(style = "display: inline-block; width: 70%;", helpText("Left")),
474474
tags$div(
475-
class = "inline-block w-70",
475+
style = "display: inline-block; width: 70%;",
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teal.widgets::optionalSliderInput(
477477
ns("pos"),
478478
label = NULL,
479479
min = 0, max = 1, value = .99, ticks = FALSE, step = .01
480480
)
481481
),
482-
tags$div(class = "inline-block w-10", helpText("Right"))
482+
tags$div(style = "display: inline-block; width: 10%;", helpText("Right"))
483483
),
484484
teal.widgets::optionalSliderInput(
485485
ns("label_size"), "Stats font size",

‎R/tm_missing_data.R‎

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@@ -184,7 +184,6 @@ tm_missing_data <- function(label = "Missing data",
184184
ui_page_missing_data <- function(id, pre_output = NULL, post_output = NULL) {
185185
ns <- NS(id)
186186
tagList(
187-
include_css_files("custom"),
188187
teal.widgets::standard_layout(
189188
output = teal.widgets::white_small_well(
190189
uiOutput(ns("dataset_tabs"))
@@ -373,9 +372,9 @@ encoding_missing_data <- function(id, summary_per_patient = FALSE, ggtheme, data
373372
uiOutput(ns("variables")),
374373
actionButton(
375374
ns("filter_na"),
376-
tags$span("Select only vars with missings", class = "whitespace-normal"),
375+
tags$span("Select only vars with missings", style = "white-space: normal;"),
377376
width = "100%",
378-
class = "mb-4"
377+
style = "margin-bottom: 1rem;"
379378
),
380379
conditionalPanel(
381380
is_tab_active_js(ns("summary_type"), "Summary"),

‎R/tm_variable_browser.R‎

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Original file line numberDiff line numberDiff line change
@@ -142,7 +142,6 @@ ui_variable_browser <- function(id,
142142
ns <- NS(id)
143143

144144
tags$div(
145-
include_css_files("custom"),
146145
shinyjs::useShinyjs(),
147146
teal.widgets::standard_layout(
148147
output = tags$div(
@@ -156,8 +155,10 @@ ui_variable_browser <- function(id,
156155
})
157156
),
158157
teal.widgets::white_small_well(
158+
### Reporter
159159
teal.reporter::add_card_button_ui(ns("add_reporter"), label = "Add Report Card"),
160160
tags$br(), tags$br(),
161+
###
161162
uiOutput(ns("ui_histogram_display")),
162163
uiOutput(ns("ui_numeric_display")),
163164
teal.widgets::plot_with_settings_ui(ns("variable_plot")),
@@ -236,11 +237,11 @@ srv_variable_browser <- function(id,
236237
tabPanel(
237238
dataname,
238239
tags$div(
239-
class = "mt-4",
240+
style = "margin-top: 1rem;",
240241
textOutput(ns(paste0("dataset_summary_", dataname)))
241242
),
242243
tags$div(
243-
class = "mt-4",
244+
style = "margin-top: 1rem;",
244245
teal.widgets::get_dt_rows(
245246
ns(paste0("variable_browser_", dataname)),
246247
ns(paste0("variable_browser_", dataname, "_rows"))

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