Gilead-BioStats · mattroumaya · Dec 5, 2022 · Nov 14, 2022 · Nov 14, 2022 · Nov 15, 2022
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -25,6 +25,7 @@ Imports:
     glue,
     gt,
     ggplot2,
+    htmlwidgets,
     here,
     janitor,
     knitr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -34,6 +34,7 @@ export(IE_Assess)
 export(IE_Map_Raw)
 export(LB_Assess)
 export(LB_Map_Raw)
+export(MakeDfConfig)
 export(MakeStratifiedAssessment)
 export(MakeWorkflowList)
 export(Make_Snapshot)
@@ -63,13 +64,20 @@ export(UpdateParams)
 export(Visualize_Scatter)
 export(Visualize_Score)
 export(Visualize_Workflow)
+export(barChart)
+export(barChartOutput)
 export(generate_md_table)
 export(is_mapping_valid)
 export(parse_data_mapping)
 export(parse_data_spec)
 export(rank_chg)
+export(renderBarChart)
+export(renderScatterPlot)
+export(scatterPlot)
+export(scatterPlotOutput)
 import(dplyr)
 import(ggplot2)
+import(htmlwidgets)
 import(purrr)
 importFrom(DiagrammeR,create_graph)
 importFrom(DiagrammeR,create_node_df)

diff --git a/R/AE_Assess.R b/R/AE_Assess.R
@@ -189,15 +189,61 @@ AE_Assess <- function(
 
     if (!hasName(lData, "dfBounds")) lData$dfBounds <- NULL
 
+
+
+    # rbm-viz setup -----------------------------------------------------------
+
+    dfConfig <- MakeDfConfig(
+      strMethod = strMethod,
+      strGroup = strGroup,
+      strAbbreviation = "AE",
+      strMetric = "AE Reporting Rate",
+      strNumerator = "AEs",
+      strDenominator = "Days on Treatment",
+      vThreshold = vThreshold
+    )
+
+
+
+      # scatter plots -----------------------------------------------------------
+
+      # ggplot bar charts -------------------------------------------------------
+
     if (strMethod != "Identity") {
+
+
       lCharts$scatter <- gsm::Visualize_Scatter(dfFlagged = lData$dfFlagged, dfBounds = lData$dfBounds, strGroupLabel = strGroup)
-      if (!bQuiet) cli::cli_alert_success("{.fn Visualize_Scatter} created {length(lCharts)} chart.")
+
+      # rbm-viz charts ----------------------------------------------------------
+      lCharts$scatterJS <- scatterPlot(
+        results = lData$dfFlagged,
+        workflow = dfConfig,
+        bounds = lData$dfBounds,
+        elementId = "aeAssessScatter"
+      )
+      if (!bQuiet) cli::cli_alert_success("Created {length(lCharts)} scatter plot{?s}.")
     }
 
-    lCharts$barMetric <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "metric")
-    lCharts$barScore <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "score", vThreshold = vThreshold)
-    if (!bQuiet) cli::cli_alert_success("{.fn Visualize_Score} created {length(names(lCharts)[names(lCharts) != 'scatter'])} chart{?s}.")
 
+      # bar charts --------------------------------------------------------------
+      lCharts$barMetric <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "metric")
+      lCharts$barScore <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "score", vThreshold = vThreshold)
+
+      lCharts$barMetricJS <- barChart(
+        results = lData$dfFlagged,
+        workflow = dfConfig,
+        yaxis = "metric",
+        elementId = "aeAssessMetric"
+      )
+
+      lCharts$barScoreJS <- barChart(
+        results = lData$dfFlagged,
+        workflow = dfConfig,
+        yaxis = "score",
+        elementId = "aeAssessScore"
+      )
+
+    if (!bQuiet) cli::cli_alert_success("Created {length(names(lCharts)[!names(lCharts) %in% c('scatter', 'scatterJS')])} bar chart{?s}.")
 
 
     # return data -------------------------------------------------------------

diff --git a/R/Consent_Assess.R b/R/Consent_Assess.R
@@ -116,9 +116,35 @@ Consent_Assess <- function(
 
     # visualizations ----------------------------------------------------------
     lCharts <- list()
+
+    dfConfig <- MakeDfConfig(
+      strMethod = "identity",
+      strGroup = strGroup,
+      strAbbreviation = "CONSENT",
+      strMetric = "Consent Issues",
+      strNumerator = "Consent Issues",
+      strDenominator = "Total Subjects",
+      vThreshold = nThreshold
+    )
+
     lCharts$barMetric <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "metric")
     lCharts$barScore <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "score")
-    if (!bQuiet) cli::cli_alert_success("{.fn Visualize_Score} created {length(lCharts)} chart{?s}.")
+
+    lCharts$barMetricJS <- barChart(
+      results = lData$dfFlagged,
+      workflow = dfConfig,
+      yaxis = "metric",
+      elementId = "consentAssessMetric"
+    )
+
+    lCharts$barScoreJS <- barChart(
+      results = lData$dfFlagged,
+      workflow = dfConfig,
+      yaxis = "score",
+      elementId = "consentAssessScore"
+    )
+
+    if (!bQuiet) cli::cli_alert_success("Created {length(lCharts)} bar chart{?s}.")
 
     # return data -------------------------------------------------------------
     return(list(

diff --git a/R/DataChg_Map_Raw.R b/R/DataChg_Map_Raw.R
@@ -37,13 +37,13 @@
 #' @export
 
 DataChg_Map_Raw <- function(
-  dfs = list(
-    dfSUBJ = clindata::rawplus_dm,
-    dfDATACHG = clindata::edc_data_change_rate
-  ),
-  lMapping = yaml::read_yaml(system.file("mappings", "mapping_edc.yaml", package = "gsm")),
-  bReturnChecks = FALSE,
-  bQuiet = TRUE
+    dfs = list(
+      dfSUBJ = clindata::rawplus_dm,
+      dfDATACHG = clindata::edc_data_change_rate
+    ),
+    lMapping = yaml::read_yaml(system.file("mappings", "mapping_edc.yaml", package = "gsm")),
+    bReturnChecks = FALSE,
+    bQuiet = TRUE
 ) {
   stopifnot(
     "bReturnChecks must be logical" = is.logical(bReturnChecks),

diff --git a/R/DataEntry_Map_Raw.R b/R/DataEntry_Map_Raw.R
@@ -37,13 +37,14 @@
 #' @export
 
 DataEntry_Map_Raw <- function(
-  dfs = list(
-    dfSUBJ = clindata::rawplus_dm,
-    dfDATAENT = clindata::edc_data_entry_lag
-  ),
-  lMapping = yaml::read_yaml(system.file("mappings", "mapping_edc.yaml", package = "gsm")),
-  bReturnChecks = FALSE,
-  bQuiet = TRUE
+    dfs = list(
+      dfSUBJ = clindata::rawplus_dm,
+      dfDATAENT = clindata::edc_data_entry_lag
+    ),
+    lMapping = yaml::read_yaml(system.file("mappings", "mapping_edc.yaml", package = "gsm")),
+    bReturnChecks = FALSE,
+    bQuiet = TRUE
+
 ) {
   stopifnot(
     "bReturnChecks must be logical" = is.logical(bReturnChecks),

diff --git a/R/Disp_Assess.R b/R/Disp_Assess.R
@@ -178,14 +178,62 @@ Disp_Assess <- function(
     if (strMethod != "QTL") {
       if (!hasName(lData, "dfBounds")) lData$dfBounds <- NULL
 
+
+
+    # rbm-viz setup -----------------------------------------------------------
+    dfConfig <- MakeDfConfig(
+      strMethod = strMethod,
+      strGroup = strGroup,
+      strAbbreviation = "DISP",
+      strMetric = "Subject Discontinuation Rate",
+      strNumerator = "Subjects Discontinued",
+      strDenominator = "Total Subjects",
+      vThreshold = vThreshold
+    )
+
+
+
       if (strMethod != "Identity") {
+
+
         lCharts$scatter <- gsm::Visualize_Scatter(dfFlagged = lData$dfFlagged, dfBounds = lData$dfBounds, strGroupLabel = strGroup)
-        if (!bQuiet) cli::cli_alert_success("{.fn Visualize_Scatter} created {length(lCharts)} chart.")
+
+        if (exists('dfBounds', lData)) {
+          bounds <- lData$dfBounds
+        } else {
+          bounds <- NULL
+        }
+
+        lCharts$scatterJS <- scatterPlot(
+          results = lData$dfFlagged,
+          workflow = dfConfig,
+          bounds = bounds,
+          elementId = "dispAssessScatter"
+        )
+        if (!bQuiet) cli::cli_alert_success("Created {length(lCharts)} scatter plot{?s}.")
       }
 
+
+    # bar charts --------------------------------------------------------------
+
       lCharts$barMetric <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "metric")
       lCharts$barScore <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "score", vThreshold = vThreshold)
-      if (!bQuiet) cli::cli_alert_success("{.fn Visualize_Score} created {length(names(lCharts)[names(lCharts) != 'scatter'])} chart{?s}.")
+
+      lCharts$barMetricJS <- barChart(
+        results = lData$dfFlagged,
+        workflow = dfConfig,
+        yaxis = "metric",
+        elementId = "dispAssessMetric"
+      )
+
+      lCharts$barScoreJS <- barChart(
+        results = lData$dfFlagged,
+        workflow = dfConfig,
+        yaxis = "score",
+        elementId = "dispAssessScore"
+      )
+
+      if (!bQuiet) cli::cli_alert_success("Created {length(names(lCharts)[!names(lCharts) %in% c('scatter', 'scatterJS')])} bar chart{?s}.")
     }
 
     # return data -------------------------------------------------------------

diff --git a/R/IE_Assess.R b/R/IE_Assess.R
@@ -107,9 +107,35 @@ IE_Assess <- function(
 
     # visualizations ----------------------------------------------------------
     lCharts <- list()
+
+    dfConfig <- MakeDfConfig(
+      strMethod = "identity",
+      strGroup = strGroup,
+      strAbbreviation = "IE",
+      strMetric = "Inclusion/Exclusion Issues (Count)",
-      strMetric = "Inclusion/Exclusion Issues (Count)",
+      strMetric = "Inclusion/Exclusion Issues",
-      strMetric = "Inclusion/Exclusion Issues (Count)",
+      strMetric = "Inclusion/Exclusion Issues",
+      strNumerator = "Inclusion/Exclusion Issues",
+      strDenominator = "Total Subjects",
+      vThreshold = nThreshold
+    )
+
     lCharts$barMetric <- Visualize_Score(dfFlagged = lData$dfFlagged, strType = "metric")
     lCharts$barScore <- Visualize_Score(dfFlagged = lData$dfFlagged, strType = "score")
-    if (!bQuiet) cli::cli_alert_success("{.fn Visualize_Score} created {length(lCharts)} chart{?s}.")
+
+    lCharts$barMetricJS <- barChart(
+      results = lData$dfFlagged,
+      workflow = dfConfig,
+      yaxis = "metric",
+      elementId = "ieAssessMetric"
+    )
+
+    lCharts$barScoreJS <- barChart(
+      results = lData$dfFlagged,
+      workflow = dfConfig,
+      yaxis = "score",
+      elementId = "ieAssessScore"
+    )
+
+    if (!bQuiet) cli::cli_alert_success("Created {length(lCharts)} bar chart{?s}.")
 
     # return data -------------------------------------------------------------
     return(list(

diff --git a/R/LB_Assess.R b/R/LB_Assess.R
@@ -168,14 +168,52 @@ LB_Assess <- function(
 
     if (!hasName(lData, "dfBounds")) lData$dfBounds <- NULL
 
+    dfConfig <- MakeDfConfig(
+      strMethod = strMethod,
+      strGroup = strGroup,
+      strAbbreviation = "LB",
+      strMetric = "LB Abnormalities (Rate)",
-      strMetric = "LB Abnormalities (Rate)",
+      strMetric = "Abnormal Lab Rate",
-      strMetric = "LB Abnormalities (Rate)",
+      strMetric = "Abnormal Lab Rate",
+      strNumerator = "Abnormal Lab Samples",
+      strDenominator = "Total Lab Samples",
+      vThreshold = vThreshold
+    )
+
+
+
     if (strMethod != "Identity") {
+
+
       lCharts$scatter <- gsm::Visualize_Scatter(dfFlagged = lData$dfFlagged, dfBounds = lData$dfBounds, strGroupLabel = strGroup)
-      if (!bQuiet) cli::cli_alert_success("{.fn Visualize_Scatter} created {length(lCharts)} chart.")
+
+      # rbm-viz charts ----------------------------------------------------------
+      lCharts$scatterJS <- scatterPlot(
+        results = lData$dfFlagged,
+        workflow = dfConfig,
+        bounds = lData$dfBounds,
+        elementId = "lbAssessScatter"
+      )
+
+      if (!bQuiet) cli::cli_alert_success("Created {length(lCharts)} scatter plot{?s}.")
     }
 
     lCharts$barMetric <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "metric")
     lCharts$barScore <- gsm::Visualize_Score(dfFlagged = lData$dfFlagged, strType = "score", vThreshold = vThreshold)
-    if (!bQuiet) cli::cli_alert_success("{.fn Visualize_Score} created {length(names(lCharts)[names(lCharts) != 'scatter'])} chart{?s}.")
+
+    lCharts$barMetricJS <- barChart(
+      results = lData$dfFlagged,
+      workflow = dfConfig,
+      yaxis = "metric",
+      elementId = "lbAssessMetric"
+    )
+
+    lCharts$barScoreJS <- barChart(
+      results = lData$dfFlagged,
+      workflow = dfConfig,
+      yaxis = "score",
+      elementId = "lbAssessScore"
+    )
+
+    if (!bQuiet) cli::cli_alert_success("Created {length(names(lCharts)[!names(lCharts) %in% c('scatter', 'scatterJS')])} bar chart{?s}.")
 
 
 

diff --git a/R/Make_Snapshot.R b/R/Make_Snapshot.R
@@ -11,7 +11,6 @@
 #' See the Data Model Vignette - Appendix 2 - Data Model Specifications for detailed specifications.
 #' @param lData `list` a named list of domain-level data frames. Names should match the values specified in `lMapping` and `lAssessments`, which are generally based on the expected inputs from `X_Map_Raw`.
 #' @param lMapping `list` Column metadata with structure `domain$key`, where `key` contains the name of the column. Default: package-defined mapping for raw+.
-
 #' @param lAssessments `list` a named list of metadata defining how each assessment should be run. By default, `MakeWorkflowList()` imports YAML specifications from `inst/workflow`.
 #' @param bUpdateParams `logical` if `TRUE`, configurable parameters found in `lMeta$config_param` will overwrite the default values in `lMeta$meta_params`. Default: `FALSE`.
 #' @param cPath `character` a character string indicating a working directory to save .csv files; the output of the snapshot.
@@ -141,6 +140,8 @@ bQuiet = TRUE
   }
 
 
+
+
   # status_site -------------------------------------------------------------
   if (!("enrolled_participants" %in% colnames(status_site))) {
     status_site_count <- gsm::Get_Enrolled(
-Original file line number
+Diff line change
@@ Expand Up / @@ -25,6 +25,7 @@ Imports: @@
         glue,
         gt,
         ggplot2,
+        htmlwidgets,
         here,
         janitor,
         knitr,
@@ Expand Down @@