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Merge pull request #11 from ohdsi-studies/develop
added shiny, hot fix for cohort 100 error
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@@ -10,3 +10,4 @@ | |
| ^LICENSE\.md$ | ||
| ^\.github$ | ||
| ^README\.Rmd$ | ||
| ^rsconnect$ | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,142 @@ | ||
| #' `runAlopeciaShiny()` launches an app to visualise TreatmentPatterns results for the alopecia study. | ||
| #' | ||
| #' @param resultsFolder Define the results folder path in character. | ||
| #' | ||
| #' @import shinythemes shinydashboard shinycssloaders shinyWidgets TreatmentPatterns here | ||
| #' @importFrom readr read_csv | ||
| #' @importFrom DT dataTableOutput renderDataTable | ||
| #' @importFrom stringr str_detect | ||
| #' @importFrom shiny shinyApp h4 uiOutput | ||
| #' @export | ||
| runShinyAlopecia <- function(resultsFolder = here::here("results")) { | ||
| ui <- dashboardPage( | ||
| dashboardHeader(title = "Menu"), | ||
| dashboardSidebar( | ||
| sidebarMenu( | ||
| menuItem( | ||
| text = "Home", | ||
| tabName = "home" | ||
| ), | ||
| menuItem( | ||
| text = "TreatmentPathways", | ||
| tabName = "data" | ||
| ) | ||
| ) | ||
| ), | ||
| dashboardBody( | ||
| tabItems( | ||
| tabItem( | ||
| tabName = "home", | ||
| h4("Analytic software to perform large-scale distributed analysis of patients with Alopecia as part of the EHDEN study-athon.") | ||
| ), | ||
| tabItem( | ||
| tabName = "data", | ||
| uiOutput("dataTable") | ||
| ) | ||
| ) | ||
| ) | ||
| ) | ||
|
|
||
| server <- function(input, output, session) { | ||
| ## TreatmentPatterns ---- | ||
| resultsPathways <- reactive({ | ||
| databases <- list.files(resultsFolder, full.names = TRUE) | ||
| resultsPathways <- list() | ||
| for (i in seq(1:length(databases))) { | ||
| # i <- 1 | ||
| targetCohorts <- list.files(databases[i], full.names = TRUE) | ||
| targetCohortNumber <- list.files(databases[i]) | ||
| for (v in seq(1:length(targetCohorts))) { | ||
| # v <- 1 | ||
| pathwaysFiles <- list.files(targetCohorts[v], full.names = TRUE) | ||
| file_metaData <- pathwaysFiles[stringr::str_detect(pathwaysFiles, "metadata")] | ||
| cdm_name <- readr::read_csv(file_metaData, show_col_types = FALSE) %>% | ||
| pull(cdmSourceName) | ||
| file_TreatmentPathways <- pathwaysFiles[stringr::str_detect(pathwaysFiles, "treatmentPathways")] | ||
| resultsPathways <- bind_rows(resultsPathways, readr::read_csv(file_TreatmentPathways, show_col_types = FALSE) %>% | ||
| mutate(cdm_name = cdm_name, | ||
| targetCohort = targetCohortNumber[v])) | ||
| } | ||
| } | ||
| return(resultsPathways) | ||
| }) | ||
|
|
||
| output$dataTable <- renderUI({ | ||
| tagList( | ||
| pickerInput( | ||
| inputId = "dataDatabase", | ||
| label = "Data partner", | ||
| choices = unique(resultsPathways()$cdm_name), | ||
| selected = unique(resultsPathways()$cdm_name)[1], | ||
| multiple = FALSE | ||
| ), | ||
| pickerInput( | ||
| inputId = "dataTargetCohort", | ||
| label = "Target Cohort", | ||
| choices = unique(resultsPathways()$targetCohort), | ||
| selected = unique(resultsPathways()$targetCohort)[1], | ||
| multiple = FALSE | ||
| ), | ||
| pickerInput( | ||
| inputId = "dataSex", | ||
| label = "Sex", | ||
| choices = unique(resultsPathways()$sex), | ||
| selected = unique(resultsPathways()$sex)[1], | ||
| multiple = FALSE | ||
| ), | ||
| pickerInput( | ||
| inputId = "dataAge", | ||
| label = "Age", | ||
| choices = unique(resultsPathways()$age), | ||
| selected = unique(resultsPathways()$age)[1], | ||
| multiple = FALSE | ||
| ), | ||
| pickerInput( | ||
| inputId = "dataIndex", | ||
| label = "Index year", | ||
| choices = unique(resultsPathways()$indexYear), | ||
| selected = unique(resultsPathways()$indexYear)[1], | ||
| multiple = FALSE | ||
| ), | ||
| tabsetPanel( | ||
| type = "tabs", | ||
| tabPanel( | ||
| "Data", | ||
| DT::dataTableOutput(outputId = "treatmentPathways") | ||
| ), | ||
| tabPanel( | ||
| "Sunburst Plot", | ||
| uiOutput(outputId = "sunburstPlot") | ||
| ) | ||
| # , | ||
| # tabPanel( | ||
| # "Sankey Diagram", | ||
| # uiOutput(outputId = "sankeyDiagram") | ||
| # ) | ||
| ) | ||
| ) | ||
| }) | ||
|
|
||
| pathwaysData <- reactive({ | ||
| resultsPathways() %>% | ||
| filter(cdm_name == input$dataDatabase, | ||
| targetCohort == input$dataTargetCohort, | ||
| sex == input$dataSex, | ||
| age == input$dataAge, | ||
| indexYear == input$dataIndex) | ||
| }) | ||
|
|
||
| output$treatmentPathways <- DT::renderDataTable(pathwaysData()) | ||
|
|
||
| output$sunburstPlot <- renderUI({ | ||
| TreatmentPatterns::createSunburstPlot2(treatmentPathways = pathwaysData(), | ||
| groupCombinations = TRUE) | ||
| }) | ||
|
|
||
| # output$sankeyDiagram <- renderUI({ | ||
| # TreatmentPatterns::createSankeyDiagram2(treatmentPathways = pathwaysData(), | ||
| # groupCombinations = TRUE) | ||
| # }) | ||
| } | ||
| shinyApp(ui, server) | ||
| } |
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