From a14dcb16a243407703d46665494bef057859da8e Mon Sep 17 00:00:00 2001 From: cecicampanile Date: Fri, 21 Feb 2025 01:06:21 +0000 Subject: [PATCH] shiny update --- shiny/data/preprocess.R | 1 + shiny/global.R | 3 + shiny/server.R | 306 ++++++---------------------------------- shiny/ui.R | 212 +++++----------------------- 4 files changed, 87 insertions(+), 435 deletions(-) diff --git a/shiny/data/preprocess.R b/shiny/data/preprocess.R index 9ebe5ff..3242044 100644 --- a/shiny/data/preprocess.R +++ b/shiny/data/preprocess.R @@ -36,3 +36,4 @@ filterValues <- defaultFilterValues(result, resultList) save(data, filterValues, file = file.path(getwd(), "data", "shinyData.RData")) rm(result, filterValues, resultList, data) + diff --git a/shiny/global.R b/shiny/global.R index b80c7e8..50a123d 100644 --- a/shiny/global.R +++ b/shiny/global.R @@ -23,6 +23,8 @@ library(yaml) # preprocess data if it has not been done fileData <- file.path(getwd(), "data", "shinyData.RData") + + if (!file.exists(fileData)) { source(file.path(getwd(), "data", "preprocess.R")) } @@ -33,5 +35,6 @@ if (!file.exists(fileData)) { # load shiny data load(fileData) + # source functions source(file.path(getwd(), "functions.R")) diff --git a/shiny/server.R b/shiny/server.R index c043f61..e96b49c 100644 --- a/shiny/server.R +++ b/shiny/server.R @@ -9,7 +9,7 @@ server <- function(input, output, session) { omopgenerics::exportSummarisedResult(data, fileName = file) } ) - + ## output summarise_omop_snapshot ----- ## output 17 ----- createOutput17 <- shiny::reactive({ @@ -32,61 +32,13 @@ server <- function(input, output, session) { # summarise_characteristics ----- - ## tidy summarise_characteristics ----- - getTidyDataSummariseCharacteristics <- shiny::reactive({ - res <- data |> - filterData("summarise_characteristics", input) |> - omopgenerics::addSettings() |> - omopgenerics::splitAll() |> - dplyr::select(!"result_id") - - - # columns to eliminate - colsEliminate <- colnames(res) - colsEliminate <- colsEliminate[!colsEliminate %in% c( - input$summarise_characteristics_tidy_columns, "variable_name", "variable_level", - "estimate_name", "estimate_type", "estimate_value" - )] - - # pivot - pivot <- input$summarise_characteristics_tidy_pivot - if (pivot != "none") { - vars <- switch(pivot, - "estimates" = "estimate_name", - "estimates and variables" = c("variable_name", "variable_level", "estimate_name") - ) - res <- res |> - visOmopResults::pivotEstimates(pivotEstimatesBy = vars) - } - - res |> - dplyr::select(!dplyr::all_of(colsEliminate)) - - }) - output$summarise_characteristics_tidy <- DT::renderDT({ - DT::datatable( - getTidyDataSummariseCharacteristics(), - options = list(scrollX = TRUE), - rownames = FALSE - ) - }) - output$summarise_characteristics_tidy_download <- shiny::downloadHandler( - filename = "tidy_summarise_characteristics.csv", - content = function(file) { - getTidyDataSummariseCharacteristics() |> - readr::write_csv(file = file) - } - ) - ## output summarise_characteristics ----- - ## output 7 ----- - createOutput7 <- shiny::reactive({ result <- data |> filterData("summarise_characteristics", input) - - if (result |> dplyr::distinct(.data$cdm_name)|>dplyr::tally()|>dplyr::pull(n)>1) header <- c("cdm_name") else header <- NULL + + if (result |> dplyr::distinct(.data$cdm_name)|>dplyr::tally()|>dplyr::pull(n)==1) header<- NULL else header <- c("cdm_name") groupColumn <- c("cohort_name", "sex") hide <- c("table_name") CohortCharacteristics::tableCharacteristics( @@ -94,19 +46,19 @@ server <- function(input, output, session) { header = header, groupColumn = groupColumn, hide = hide, - type = "datatable" + type = "gt" ) - + }) - output$summarise_characteristics_gt_7 <- DT::renderDT({ + output$summarise_characteristics_gt_7 <- gt::render_gt({ createOutput7() }) output$summarise_characteristics_gt_7_download <- shiny::downloadHandler( filename = paste0("output_gt_summarise_characteristics.", input$summarise_characteristics_gt_7_download_type), content = function(file) { createOutput7() |> - readr::write_csv(file = file) + gt::gtsave(file = file) } ) @@ -151,7 +103,6 @@ server <- function(input, output, session) { dplyr::select(!"result_id")|> dplyr::mutate(estimate_value = suppressWarnings(dplyr::if_else(.data$estimate_value == "-", NA_integer_, as.numeric(.data$estimate_value)))) - # columns to eliminate colsEliminate <- colnames(res) colsEliminate <- colsEliminate[!colsEliminate %in% c( @@ -164,17 +115,15 @@ server <- function(input, output, session) { if (pivot != "none") { vars <- switch(pivot, "estimates" = "estimate_name", - "estimates and variables" = c("variable_name", "estimate_name") ) res <- res |> visOmopResults::pivotEstimates(pivotEstimatesBy = vars) - } + } res |> dplyr::select(!dplyr::any_of(colsEliminate)) }) output$summarise_missing_data_tidy <- DT::renderDT({ - DT::datatable( getTidyDataSummariseMissingData(), options = list(scrollX = TRUE), @@ -227,7 +176,9 @@ server <- function(input, output, session) { filterData("summarise_concept_id_counts", input) |> omopgenerics::addSettings() |> omopgenerics::splitAll() |> - dplyr::select(!"result_id") + dplyr::select(!"result_id")|> + dplyr::mutate(estimate_value = suppressWarnings(dplyr::if_else(.data$estimate_value == "-", NA_integer_, as.numeric(.data$estimate_value)))) + # columns to eliminate colsEliminate <- colnames(res) @@ -240,16 +191,14 @@ server <- function(input, output, session) { pivot <- input$summarise_concept_id_counts_tidy_pivot if (pivot != "none") { vars <- switch(pivot, - "estimates" = "estimate_name", - "estimates and variables" = c("variable_name", "variable_level", "estimate_name") + "estimates" = "estimate_name" ) - res <- res |> + res <- res |> visOmopResults::pivotEstimates(pivotEstimatesBy = vars) - } + } res |> - dplyr::select(!dplyr::all_of(colsEliminate))|> - dplyr::mutate(estimate_value = dplyr::if_else(.data$estimate_value!= "-", as.numeric(.data$estimate_value), NA_real_)) + dplyr::select(!dplyr::all_of(colsEliminate)) }) output$summarise_concept_id_counts_tidy <- DT::renderDT({ DT::datatable( @@ -295,9 +244,6 @@ server <- function(input, output, session) { # } # ) - - # summarise_clinical_records ----- - ## tidy summarise_clinical_records ----- getTidyDataSummariseClinicalRecords <- shiny::reactive({ res <- data |> filterData("summarise_clinical_records", input) |> @@ -308,7 +254,7 @@ server <- function(input, output, session) { # columns to eliminate colsEliminate <- colnames(res) colsEliminate <- colsEliminate[!colsEliminate %in% c( - input$summarise_clinical_records_tidy_columns, "variable_name", "variable_level", + input$summarise_clinical_records_tidy_columns, "variable_name", "estimate_name", "estimate_type", "estimate_value" )] @@ -316,8 +262,8 @@ server <- function(input, output, session) { pivot <- input$summarise_clinical_records_tidy_pivot if (pivot != "none") { vars <- switch(pivot, - "estimates" = "estimate_name", - "estimates and variables" = c("variable_name", "variable_level", "estimate_name") + "estimates" = c("estimate_name"), + "estimates and variables" = c("variable_name", "estimate_name") ) res <- res |> visOmopResults::pivotEstimates(pivotEstimatesBy = vars) @@ -339,130 +285,58 @@ server <- function(input, output, session) { getTidyDataSummariseClinicalRecords() |> readr::write_csv(file = file) } - ) - ## output summarise_clinical_records ----- - ## output 0 ----- - # createOutput22 <- shiny::reactive({ - # result <- data |> - # filterData("summarise_clinical_records", input) - # - # header <- input$summarise_clinical_records_gt_0_header - # group <- input$summarise_clinical_records_gt_0_group - # hide <- input$summarise_clinical_records_gt_0_hide - # - # if (is.null(header) || length(header) == 0) header <- c("cdm_name") - # if (is.null(group) || length(group) == 0) group <- c() - # if (is.null(hide) || length(hide) == 0) hide <- c() - # - # simpleTable( - # result, - # header = header, - # group = group, - # hide = hide - # ) - # }) - # output$summarise_clinical_records_gt_0 <- gt::render_gt({ - # createOutput22() - # }) - # output$summarise_clinical_records_gt_0_download <- shiny::downloadHandler( - # filename = paste0("output_gt_summarise_clinical_records.", input$summarise_clinical_records_gt_0_download_type), - # content = function(file) { - # obj <- createOutput22() - # gt::gtsave(data = obj, filename = file) - # } - # ) + ) + + createOutput21 <- shiny::reactive({ res <- data |> filterData("summarise_clinical_records", input) - tableClinicalRecordsLocal(res, type = "datatable") + tableClinicalRecordsLocal(res, type = "gt") }) - output$summarise_clinical_records_gt_15 <- DT::renderDataTable({ + output$summarise_clinical_records_gt_15 <- gt::render_gt({ + + createOutput21() - createOutput21() - }) output$summarise_clinical_records_gt_15_download <- shiny::downloadHandler( filename = paste0("output_gt_summarise_clinical_records.", input$summarise_clinical_records_gt_15_download_type), content = function(file) { createOutput21() |> - readr::write_csv(file = file) + gt::gtsave(file = file) } ) - # summarise_record_count ----- - ## tidy summarise_record_count ----- - getTidyDataSummariseRecordCount <- shiny::reactive({ - res <- data |> - filterData("summarise_record_count", input) |> - omopgenerics::addSettings() |> - omopgenerics::splitAll() |> - dplyr::select(!"result_id") - - # columns to eliminate - colsEliminate <- colnames(res) - colsEliminate <- colsEliminate[!colsEliminate %in% c( - input$summarise_record_count_tidy_columns, "variable_name", "variable_level", - "estimate_name", "estimate_type", "estimate_value" - )] - - # pivot - pivot <- input$summarise_record_count_tidy_pivot - if (pivot != "none") { - vars <- switch(pivot, - "estimates" = "estimate_name", - "estimates and variables" = c("variable_name", "variable_level", "estimate_name") - ) - res <- res |> - visOmopResults::pivotEstimates(pivotEstimatesBy = vars) - } - - res |> - dplyr::select(!dplyr::all_of(colsEliminate)) - }) - output$summarise_record_count_tidy <- DT::renderDT({ - DT::datatable( - getTidyDataSummariseRecordCount(), - options = list(scrollX = TRUE), - rownames = FALSE - ) - }) - output$summarise_record_count_tidy_download <- shiny::downloadHandler( - filename = "tidy_summarise_record_count.csv", - content = function(file) { - getTidyDataSummariseRecordCount() |> - readr::write_csv(file = file) - } - ) + ## output summarise_record_count ----- ## output 0 ----- createOutput23 <- shiny::reactive({ result <- data |> filterData("summarise_record_count", input)|> dplyr::arrange(.data$additional_level) - - if (result |> dplyr::distinct(.data$cdm_name)|>dplyr::tally()|>dplyr::pull(n)>1) header <- c("cdm_name") else header <- NULL - group <- c("omop_table", "sex", "age_group") - hide <- c("interval", "study_period_end", "study_period_start", "variable_level", "estimate_name") + + header <- c("cdm_name", "Number records" ) + group <- c("omop_table" ) + hide <- c("interval", "study_period_end", "study_period_start", "variable_level", "estimate_name", "variable_name" ) simpleTable( result, header = header, group = group, hide = hide, - type = "datatable", - estimateNumeric = TRUE + type = "gt", + estimateNumeric = FALSE ) }) - output$summarise_record_count_gt_0 <- DT::renderDataTable({ + output$summarise_record_count_gt_0 <- gt::render_gt({ createOutput23() }) output$summarise_record_count_gt_0_download <- shiny::downloadHandler( filename = paste0("output_gt_summarise_record_count.", input$summarise_record_count_gt_0_download_type), content = function(file) { createOutput23()|> - readr::write_csv(file = file) + gt::gtsave(filename = file) } ) @@ -494,75 +368,32 @@ server <- function(input, output, session) { ) - # summarise_in_observation ----- - ## tidy summarise_in_observation ----- - getTidyDataSummariseInObservation <- shiny::reactive({ - res <- data |> - filterData("summarise_in_observation", input) |> - omopgenerics::addSettings() |> - omopgenerics::splitAll() |> - dplyr::select(!"result_id") - - # columns to eliminate - colsEliminate <- colnames(res) - colsEliminate <- colsEliminate[!colsEliminate %in% c( - input$summarise_in_observation_tidy_columns, "variable_name", "variable_level", - "estimate_name", "estimate_type", "estimate_value" - )] - - # pivot - pivot <- input$summarise_in_observation_tidy_pivot - if (pivot != "none") { - vars <- switch(pivot, - "estimates" = "estimate_name", - "estimates and variables" = c("variable_name", "variable_level", "estimate_name") - ) - res <- res |> - visOmopResults::pivotEstimates(pivotEstimatesBy = vars) - } - - res |> - dplyr::select(!dplyr::all_of(colsEliminate)) - }) - output$summarise_in_observation_tidy <- DT::renderDT({ - DT::datatable( - getTidyDataSummariseInObservation(), - options = list(scrollX = TRUE), - rownames = FALSE - ) - }) - output$summarise_in_observation_tidy_download <- shiny::downloadHandler( - filename = "tidy_summarise_in_observation.csv", - content = function(file) { - getTidyDataSummariseInObservation() |> - readr::write_csv(file = file) - } - ) + ## output summarise_in_observation ----- ## output 0 ----- createOutput0 <- shiny::reactive({ result <- data |> filterData("summarise_in_observation", input) - - if (result |> dplyr::distinct(.data$cdm_name)|>dplyr::tally()|>dplyr::pull(n)>1) header <- c("cdm_name") else header <- NULL - group <- c("sex", "age_group") - hide <- c("omop_table", "interval", "study_period_end", "study_period_start", "variable_level") + + header<-c("cdm_name") + group <- c("time_interval") + hide <- c("omop_table", "interval", "study_period_end", "study_period_start", "variable_level","estimate_name" ) simpleTable( result, header = header, group = group, hide = hide, - type = "datatable" + type = "gt" ) }) - output$summarise_in_observation_gt_0 <- DT::renderDataTable({ + output$summarise_in_observation_gt_0 <- gt::render_gt({ createOutput0() }) output$summarise_in_observation_gt_0_download <- shiny::downloadHandler( filename = paste0("output_gt_summarise_in_observation.", input$summarise_in_observation_gt_0_download_type), content = function(file) { createOutput0() |> - readr::write_csv(file = file) + gt::gtsave(file = file) } ) @@ -599,50 +430,7 @@ server <- function(input, output, session) { } ) - # summarise_observation_period ----- - ## tidy summarise_observation_period ----- - getTidyDataSummariseObservationPeriod <- shiny::reactive({ - res <- data |> - filterData("summarise_observation_period", input) |> - omopgenerics::addSettings() |> - omopgenerics::splitAll() |> - dplyr::select(!"result_id") - - # columns to eliminate - colsEliminate <- colnames(res) - colsEliminate <- colsEliminate[!colsEliminate %in% c( - input$summarise_observation_period_tidy_columns, "variable_name", "variable_level", - "estimate_name", "estimate_type", "estimate_value" - )] - - # pivot - pivot <- input$summarise_observation_period_tidy_pivot - if (pivot != "none") { - vars <- switch(pivot, - "estimates" = "estimate_name", - "estimates and variables" = c("variable_name", "variable_level", "estimate_name") - ) - res <- res |> - visOmopResults::pivotEstimates(pivotEstimatesBy = vars) - } - - res |> - dplyr::select(!dplyr::all_of(colsEliminate)) - }) - output$summarise_observation_period_tidy <- DT::renderDT({ - DT::datatable( - getTidyDataSummariseObservationPeriod(), - options = list(scrollX = TRUE), - rownames = FALSE - ) - }) - output$summarise_observation_period_tidy_download <- shiny::downloadHandler( - filename = "tidy_summarise_observation_period.csv", - content = function(file) { - getTidyDataSummariseObservationPeriod() |> - readr::write_csv(file = file) - } - ) + ## output summarise_observation_period ----- ## output 15 ----- createOutput15 <- shiny::reactive({ @@ -652,17 +440,17 @@ server <- function(input, output, session) { tableObservationPeriodLocal( result, - type = "datatable" + type = "gt" ) }) - output$summarise_observation_period_gt_15 <- DT::renderDataTable({ + output$summarise_observation_period_gt_15 <- gt::render_gt({ createOutput15() }) output$summarise_observation_period_gt_15_download <- shiny::downloadHandler( filename = paste0("output_gt_summarise_observation_period.", input$summarise_observation_period_gt_15_download_type), content = function(file) { createOutput15() |> - readr::write_csv(file = file) + gt::gtsave(filename = file) } ) diff --git a/shiny/ui.R b/shiny/ui.R index 1068135..eb0c26f 100644 --- a/shiny/ui.R +++ b/shiny/ui.R @@ -12,7 +12,7 @@ ui <- bslib::page_navbar( ), "" ), - theme = bslib::bs_theme(preset = "cerulean"), #cerulean + theme = bslib::bs_theme(bootswatch = "flatly"), #cerulean bslib::nav_panel( title = "Background", icon = shiny::icon("disease"), @@ -112,7 +112,7 @@ ui <- bslib::page_navbar( inputId = "summarise_characteristics_grouping_sex", label = "Sex", choices = filterValues$summarise_characteristics_grouping_sex, - selected = filterValues$summarise_characteristics_grouping_sex, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -150,39 +150,6 @@ ui <- bslib::page_navbar( ) ), bslib::navset_card_tab( - bslib::nav_panel( - title = "Tidy", - bslib::card( - full_screen = TRUE, - bslib::card_header( - bslib::popover( - shiny::icon("download"), - shiny::downloadButton(outputId = "summarise_characteristics_tidy_download", label = "Download csv") - ), - class = "text-end" - ), - bslib::layout_sidebar( - sidebar = bslib::sidebar( - shinyWidgets::pickerInput( - inputId = "summarise_characteristics_tidy_columns", - label = "Columns", - choices = filterValues$summarise_characteristics_tidy_columns, - selected = filterValues$summarise_characteristics_tidy_columns, - multiple = TRUE, - options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") - ), - shiny::radioButtons( - inputId = "summarise_characteristics_tidy_pivot", - label = "Pivot estimates/variables", - choices = c("none", "estimates", "estimates and variables"), - selected = "none" - ), - position = "right" - ), - DT::dataTableOutput("summarise_characteristics_tidy") - ) - ) - ), bslib::nav_panel( title = "Formatted", bslib::card( @@ -228,7 +195,7 @@ ui <- bslib::page_navbar( # ), # position = "right" # ), - DT::dataTableOutput("summarise_characteristics_gt_7") + gt::gt_output("summarise_characteristics_gt_7") ) ), @@ -329,7 +296,7 @@ ui <- bslib::page_navbar( inputId = "summarise_missing_data_grouping_omop_table", label = "Omop table", choices = filterValues$summarise_missing_data_grouping_omop_table, - selected = filterValues$summarise_missing_data_grouping_omop_table, + selected = c("drug_exposure"), multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -337,7 +304,7 @@ ui <- bslib::page_navbar( inputId = "summarise_missing_data_grouping_age_group", label = "Age group", choices = filterValues$summarise_missing_data_grouping_age_group, - selected = filterValues$summarise_missing_data_grouping_age_group, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -345,7 +312,7 @@ ui <- bslib::page_navbar( inputId = "summarise_missing_data_grouping_sex", label = "Sex", choices = filterValues$summarise_missing_data_grouping_sex, - selected = filterValues$summarise_missing_data_grouping_sex, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -353,7 +320,7 @@ ui <- bslib::page_navbar( inputId = "summarise_missing_data_grouping_year", label = "Year", choices = filterValues$summarise_missing_data_grouping_year, - selected = filterValues$summarise_missing_data_grouping_year, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ) @@ -400,14 +367,14 @@ ui <- bslib::page_navbar( inputId = "summarise_missing_data_tidy_columns", label = "Columns", choices = filterValues$summarise_missing_data_tidy_columns, - selected = filterValues$summarise_missing_data_tidy_columns, + selected = c("cdm_name", "omop_table", "age_group","sex", "year", "variable_name", "estimate_name", "estimate_value"), multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), shiny::radioButtons( inputId = "summarise_missing_data_tidy_pivot", label = "Pivot estimates/variables", - choices = c("none", "estimates", "estimates and variables"), + choices = c("none", "estimates"), selected = "none" ), position = "right" @@ -446,7 +413,7 @@ ui <- bslib::page_navbar( inputId = "summarise_clinical_records_grouping_age_group", label = "Age group", choices = filterValues$summarise_clinical_records_grouping_age_group, - selected = filterValues$summarise_clinical_records_grouping_age_group, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -454,7 +421,7 @@ ui <- bslib::page_navbar( inputId = "summarise_clinical_records_grouping_sex", label = "Sex", choices = filterValues$summarise_clinical_records_grouping_sex, - selected = filterValues$summarise_clinical_records_grouping_sex, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ) @@ -501,14 +468,14 @@ ui <- bslib::page_navbar( inputId = "summarise_clinical_records_tidy_columns", label = "Columns", choices = filterValues$summarise_clinical_records_tidy_columns, - selected = filterValues$summarise_clinical_records_tidy_columns, + selected = c("cdm_name", "omop_table", "age_group","sex", "year", "variable_name","variable_level", "estimate_name", "estimate_value"), multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), shiny::radioButtons( inputId = "summarise_clinical_records_tidy_pivot", label = "Pivot estimates/variables", - choices = c("none", "estimates", "estimates and variables"), + choices = c("none","estimates","estimates and variables"), selected = "none" ), position = "right" @@ -584,7 +551,7 @@ ui <- bslib::page_navbar( ), class = "text-end" ), - DT::dataTableOutput("summarise_clinical_records_gt_15") + gt::gt_output("summarise_clinical_records_gt_15") ) ) @@ -618,7 +585,7 @@ ui <- bslib::page_navbar( inputId = "summarise_record_count_grouping_age_group", label = "Age group", choices = filterValues$summarise_record_count_grouping_age_group, - selected = filterValues$summarise_record_count_grouping_age_group, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -626,7 +593,7 @@ ui <- bslib::page_navbar( inputId = "summarise_record_count_grouping_sex", label = "Sex", choices = filterValues$summarise_record_count_grouping_sex, - selected = filterValues$summarise_record_count_grouping_sex, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -634,7 +601,7 @@ ui <- bslib::page_navbar( inputId = "summarise_record_count_grouping_time_interval", label = "Time interval", choices = filterValues$summarise_record_count_grouping_time_interval, - selected = filterValues$summarise_record_count_grouping_time_interval, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ) @@ -664,39 +631,7 @@ ui <- bslib::page_navbar( ) ), bslib::navset_card_tab( - bslib::nav_panel( - title = "Tidy", - bslib::card( - full_screen = TRUE, - bslib::card_header( - bslib::popover( - shiny::icon("download"), - shiny::downloadButton(outputId = "summarise_record_count_tidy_download", label = "Download csv") - ), - class = "text-end" - ), - bslib::layout_sidebar( - sidebar = bslib::sidebar( - shinyWidgets::pickerInput( - inputId = "summarise_record_count_tidy_columns", - label = "Columns", - choices = filterValues$summarise_record_count_tidy_columns, - selected = filterValues$summarise_record_count_tidy_columns, - multiple = TRUE, - options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") - ), - shiny::radioButtons( - inputId = "summarise_record_count_tidy_pivot", - label = "Pivot estimates/variables", - choices = c("none", "estimates", "estimates and variables"), - selected = "none" - ), - position = "right" - ), - DT::dataTableOutput("summarise_record_count_tidy") - ) - ) - ), + bslib::nav_panel( title = "Formatted", bslib::card( @@ -742,7 +677,7 @@ ui <- bslib::page_navbar( # ), # position = "right" # ), - DT::dataTableOutput("summarise_record_count_gt_0") + gt::gt_output("summarise_record_count_gt_0") #) ) ), @@ -784,9 +719,9 @@ ui <- bslib::page_navbar( shiny::selectizeInput( inputId = "summarise_record_count_ggplot2_16_colour", label = "Colour", - selected = "cdm_name", + selected = "omop_table", multiple = TRUE, - choices = c("cdm_name", "age_group", "sex"), + choices = c("cdm_name", "age_group", "sex", "omop_table"), options = list(plugins = "remove_button") ), shiny::selectizeInput( @@ -794,7 +729,7 @@ ui <- bslib::page_navbar( label = "Facet", selected = "cdm_name", multiple = TRUE, - choices = c("cdm_name", "age_group", "sex"), + choices = c("cdm_name", "age_group", "sex", "omop_table"), options = list(plugins = "remove_button") ), position = "right" @@ -825,7 +760,7 @@ ui <- bslib::page_navbar( inputId = "summarise_concept_id_counts_grouping_omop_table", label = "Omop table", choices = filterValues$summarise_concept_id_counts_grouping_omop_table, - selected = filterValues$summarise_concept_id_counts_grouping_omop_table, + selected = c("drug_exposure"), multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -833,7 +768,7 @@ ui <- bslib::page_navbar( inputId = "summarise_concept_id_counts_grouping_age_group", label = "Age group", choices = filterValues$summarise_concept_id_counts_grouping_age_group, - selected = filterValues$summarise_concept_id_counts_grouping_age_group, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -841,7 +776,7 @@ ui <- bslib::page_navbar( inputId = "summarise_concept_id_counts_grouping_sex", label = "Sex", choices = filterValues$summarise_concept_id_counts_grouping_sex, - selected = filterValues$summarise_concept_id_counts_grouping_sex, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -849,18 +784,7 @@ ui <- bslib::page_navbar( inputId = "summarise_concept_id_counts_grouping_year", label = "Year", choices = filterValues$summarise_concept_id_counts_grouping_year, - selected = filterValues$summarise_concept_id_counts_grouping_year, - multiple = TRUE, - options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") - ) - ), - bslib::accordion_panel( - title = "Variables", - shinyWidgets::pickerInput( - inputId = "summarise_concept_id_counts_variable_name", - label = "Variable name", - choices = filterValues$summarise_concept_id_counts_variable_name, - selected = filterValues$summarise_concept_id_counts_variable_name, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ) @@ -895,7 +819,7 @@ ui <- bslib::page_navbar( shinyWidgets::pickerInput( inputId = "summarise_concept_id_counts_tidy_columns", label = "Columns", - choices = filterValues$summarise_concept_id_counts_tidy_columns, + choices = c("cdm_name", "omop_table", "age_group","sex", "year", "variable_name","variable_level", "estimate_name", "estimate_value"), selected = filterValues$summarise_concept_id_counts_tidy_columns, multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") @@ -903,7 +827,7 @@ ui <- bslib::page_navbar( shiny::radioButtons( inputId = "summarise_concept_id_counts_tidy_pivot", label = "Pivot estimates/variables", - choices = c("none", "estimates", "estimates and variables"), + choices = c("none", "estimates"), selected = "none" ), position = "right" @@ -945,7 +869,7 @@ ui <- bslib::page_navbar( inputId = "summarise_in_observation_grouping_sex", label = "Sex", choices = filterValues$summarise_in_observation_grouping_sex, - selected = filterValues$summarise_in_observation_grouping_sex, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -953,7 +877,7 @@ ui <- bslib::page_navbar( inputId = "summarise_in_observation_grouping_age_group", label = "Age group", choices = filterValues$summarise_in_observation_grouping_age_group, - selected = filterValues$summarise_in_observation_grouping_age_group, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -991,39 +915,7 @@ ui <- bslib::page_navbar( ) ), bslib::navset_card_tab( - bslib::nav_panel( - title = "Tidy", - bslib::card( - full_screen = TRUE, - bslib::card_header( - bslib::popover( - shiny::icon("download"), - shiny::downloadButton(outputId = "summarise_in_observation_tidy_download", label = "Download csv") - ), - class = "text-end" - ), - bslib::layout_sidebar( - sidebar = bslib::sidebar( - shinyWidgets::pickerInput( - inputId = "summarise_in_observation_tidy_columns", - label = "Columns", - choices = filterValues$summarise_in_observation_tidy_columns, - selected = filterValues$summarise_in_observation_tidy_columns, - multiple = TRUE, - options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") - ), - shiny::radioButtons( - inputId = "summarise_in_observation_tidy_pivot", - label = "Pivot estimates/variables", - choices = c("none", "estimates", "estimates and variables"), - selected = "none" - ), - position = "right" - ), - DT::dataTableOutput("summarise_in_observation_tidy") - ) - ) - ), + bslib::nav_panel( title = "Formatted", bslib::card( @@ -1069,7 +961,7 @@ ui <- bslib::page_navbar( # ), # position = "right" # ), - DT::dataTableOutput("summarise_in_observation_gt_0") + gt::gt_output("summarise_in_observation_gt_0") #) ) ), @@ -1171,7 +1063,7 @@ ui <- bslib::page_navbar( inputId = "summarise_observation_period_grouping_age_group", label = "Age group", choices = filterValues$summarise_observation_period_grouping_age_group, - selected = filterValues$summarise_observation_period_grouping_age_group, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ), @@ -1179,7 +1071,7 @@ ui <- bslib::page_navbar( inputId = "summarise_observation_period_grouping_sex", label = "Sex", choices = filterValues$summarise_observation_period_grouping_sex, - selected = filterValues$summarise_observation_period_grouping_sex, + selected = "overall", multiple = TRUE, options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") ) @@ -1209,39 +1101,7 @@ ui <- bslib::page_navbar( ) ), bslib::navset_card_tab( - bslib::nav_panel( - title = "Tidy", - bslib::card( - full_screen = TRUE, - bslib::card_header( - bslib::popover( - shiny::icon("download"), - shiny::downloadButton(outputId = "summarise_observation_period_tidy_download", label = "Download csv") - ), - class = "text-end" - ), - bslib::layout_sidebar( - sidebar = bslib::sidebar( - shinyWidgets::pickerInput( - inputId = "summarise_observation_period_tidy_columns", - label = "Columns", - choices = filterValues$summarise_observation_period_tidy_columns, - selected = filterValues$summarise_observation_period_tidy_columns, - multiple = TRUE, - options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3") - ), - shiny::radioButtons( - inputId = "summarise_observation_period_tidy_pivot", - label = "Pivot estimates/variables", - choices = c("none", "estimates", "estimates and variables"), - selected = "none" - ), - position = "right" - ), - DT::dataTableOutput("summarise_observation_period_tidy") - ) - ) - ), + bslib::nav_panel( title = "Formatted", bslib::card( @@ -1260,7 +1120,7 @@ ui <- bslib::page_navbar( ), class = "text-end" ), - DT::dataTableOutput("summarise_observation_period_gt_15") + gt::gt_output("summarise_observation_period_gt_15") ) ), bslib::nav_panel(