Merge pull request #20 from ASA-DIA-InteractiveSafetyGraphics/v0.2.1-dev

V0.2.1 dev
SafetyGraphics · Oct 24, 2018 · 4953342 · 4953342
2 parents a3a4716 + 32b0fae
commit 4953342
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Showing 9 changed files with 3,633 additions and 2,663 deletions.
diff --git a/.gitignore b/.gitignore
@@ -35,3 +35,5 @@ vignettes/*.pdf
 # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
 rsconnect/
 .Rproj.user
+
+.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ReDish
 Title: Create an interactive graphic for the Evaluation of Drug-Induced Serious Hepatotoxicity (eDISH).
-Version: 0.0.1
+Version: 0.2.1
 Authors@R: c(
 	person("Becca", "Krouse", email = "rebecca_krouse@rhoworld.com", role = c("cre","aut")),
 	person("Jeremy", "Wildfire", role = "aut"),

diff --git a/R/eDISH.R b/R/eDISH.R
@@ -6,11 +6,11 @@
 #' @param id_col Unique subject identifier variable name. Default: \code{"USUBJID"}.
 #' @param value_col Lab result variable name. Default: \code{"STRESN"}. 
 #' @param measure_col Lab measure variable name. Default: \code{"TEST"}.
-#' @param unit_col Lab measure unit variable name. Default: \code{"STRESU"}.
 #' @param normal_col_low Lower limit of normal variable name. Default: \code{"STNRLO"}.
 #' @param normal_col_high Upper limit of normal variable name. Default: \code{"STNRHI"}. 
 #' @param visit_col Visit variable name. Default: \code{"VISIT"}.
 #' @param visitn_col Visit number variable name. Default: \code{"VISITN"}. 
+#' @param studyday_col  Visit day variable name. Default: \code{"DY"}. 
 #' @param baseline_visitn Value of baseline visit number. Used to calculate mDish. Default: \code{1}. 
 #' @param filters An optional data frame of filters ("value_col") and associated metadata ("label"). Default: \code{NULL}.
 #' @param group_cols An optional data frame of filters ("value_col") and associated metadata ("label"). Default: \code{NULL}.
@@ -21,6 +21,7 @@
 #' When multiple options are specified, a control allowing the user to interactively change the x variable is shown. Default: \code{c("ALT", "AST", "ALP")}.
 #' @param y_options Specifies variable options for the y-axis using the key values from \code{measure_values} (e.g. "TB"). 
 #' When multiple options are specified, a control allowing the user to interactively change the y variable is shown. Default: \code{c("TB", "ALP")}.
+#' @param analysisFlag An optional list defining which column \code{value_col} and values \code{values} should be used to records for use in eDish and mDish analyses. Default: \code{NULL}.
 #' @param visit_window Default visit window used to highlight eDish points where x and y measures occurred within the specified number of days. 
 #' Editable by user after render. Default: \code{30}.
 #' @param r_ratio_filter Specifies whether the R Ratio filter should be shown. R ratio is defined as: 
@@ -42,7 +43,9 @@
 #'       id_col = "USUBJID",
 #'       value_col = "AVAL", 
 #'       measure_col = "PARAM", 
+#'       visit_col = "VISIT",
 #'       visitn_col = "VISITNUM", 
+#'       studyday_col = "ADY",
 #'       normal_col_low = "A1LO", 
 #'       normal_col_high = "A1HI", 
 #'       measure_values = list(ALT = "Alanine Aminotransferase (U/L)",
@@ -61,7 +64,9 @@
 #' settingsl <- list(id_col = "USUBJID",
 #'       value_col = "AVAL", 
 #'       measure_col = "PARAM", 
-#'       visitn_col = "VISITNUM", 
+#'       visit_col = "VISIT",
+#'       visitn_col = "VISITNUM",
+#'       studyday_col = "ADY", 
 #'       normal_col_low = "A1LO", 
 #'       normal_col_high = "A1HI", 
 #'       group_cols = group_cols_vec,
@@ -81,20 +86,21 @@ eDISH <- function(data,
                   id_col = "USUBJID",
                   value_col = "STRESN",
                   measure_col = "TEST",
-                  unit_col = "STRESU",
                   normal_col_low = "STNRLO",
                   normal_col_high = "STNRHI",
                   visit_col = "VISIT",
                   visitn_col = "VISITN",
+                  studyday_col = "DY",
                   baseline_visitn = 1,
                   filters = NULL,
                   group_cols = NULL,
+                  analysisFlag= NULL,
                   measure_values = list(ALT = "Aminotransferase, alanine (ALT)",
                                         AST = "Aminotransferase, aspartate (AST)",
                                         TB = "Total Bilirubin",
                                         ALP = "Alkaline phosphatase (ALP)"),
                   x_options = c("ALT", "AST", "ALP"),
-                  y_options = c("TB", "ALP"), # temporarily making this a vector of length 2 until JS side fixed
+                  y_options =  "TB", 
                   visit_window = 30,
                   r_ratio_filter = TRUE,
                   r_ratio_cut = 0,
@@ -112,14 +118,15 @@ eDISH <- function(data,
           id_col = id_col, 
           value_col = value_col,
           measure_col = measure_col,
-          unit_col = unit_col,
           normal_col_low = normal_col_low,
           normal_col_high = normal_col_high,
           visit_col = visit_col,
           visitn_col = visitn_col,
+          studyday_col = studyday_col,
           baseline_visitn = baseline_visitn,
           filters = filters,
           group_cols = group_cols,
+          analysisFlag = analysisFlag,
           measure_values = measure_values,
           x_options = x_options,
           y_options = y_options,

diff --git a/inst/htmlwidgets/eDISH.js b/inst/htmlwidgets/eDISH.js
@@ -1,8 +1,8 @@
 HTMLWidgets.widget({
 
-  name: 'eDISH',
+  name: "eDISH",
 
-  type: 'output',
+  type: "output",
 
   factory: function(el, width, height) {
 
@@ -11,74 +11,16 @@ HTMLWidgets.widget({
     return {
 
       renderValue: function(rSettings) {
-
-
         el.innerHTML = "<div class='edish'></div>";
-
+        
         let settings = rSettings.settings;
         settings.max_width = 600;
-
-       // let settings = {
-        //    max_width: 600,
-           // value_col: 'AVAL',
-           // measure_col: 'PARAM',
-           // visitn_col: 'VISITNUM',
-           //studyday_col: 'ADY',
-           //normal_col_low: 'A1LO',
-           // normal_col_high: 'A1HI',
-           // id_col: 'USUBJID',
-           // group_cols: ['TRTA','RACE','AGEGR1'],
-           // filters: [
-           //     {
-           //         value_col: 'TRTA',
-          //          label: 'Treatment'
-          //     },
-          //      {
-          //          value_col: 'SEX',
-         //           label: 'Sex'
-         //       },
-         //       {
-         //           value_col: 'RACE',
-         //           label: 'Race'
-         //       },
-         //       {
-         //           value_col: 'AGEGR1',
-         //           label: 'Age group'
-        //        },
-        //    ],
-       //              //   measure_values:{
-        //     'ALT':'Alanine Aminotransferase (U/L)',
-        //      'AST':'Aspartate Aminotransferase (U/L)',
-        //     'TB':'Bilirubin (umol/L)',
-        //    'ALP':'Alkaline Phosphatase (U/L)'
-        //   }
-       //     value_col: rSettings.settings.value_col,
-       //     measure_col: rSettings.settings.measure_col,
-         //   visitn_col: rSettings.settings.visitn_col,
-           // normal_col_low: rSettings.settings.normal_col_low,
-      //      normal_col_high: rSettings.settings.normal_col_high,
-      //      id_col: rSettings.settings.id_col,
-      //      baseline_visitn: rSettings.settings.baseline_visitn,
-      //      filters: rSettings.settings.filters,
-      //      group_cols: rSettings.settings.group_cols,
-      //      measure_values: rSettings.settings.measure_values,
-      //      x_options: rSettings.settings.x_options,
-      //      y_options: rSettings.settings.y_options,
-      //      measure_bounds: rSettings.settings.measure_bounds,
-      //      visit_window: rSettings.settings.visit_window,
-      //      r_ratio_filter: rSettings.settings.r_ratio_filter,
-      //      r_ratio_cut: rSettings.settings.r_ratio_cut,
-      //      showTitle: rSettings.settings.showTitle,
-      //      warningText: rSettings.settings.warningText
-      //  };
-
-         rSettings.data = HTMLWidgets.dataframeToD3(rSettings.data);
+        rSettings.data = HTMLWidgets.dataframeToD3(rSettings.data);
 
+        // console.log(settings);
+        // console.log(rSettings);
 
-         console.log(settings);
-         console.log(rSettings);
-
-        safetyedish('.edish', settings).init(rSettings.data);
+        safetyedish(".edish", settings).init(rSettings.data);
 
       },
 
@@ -90,4 +32,4 @@ HTMLWidgets.widget({
 
     };
   }
-});
+});
diff --git a/inst/htmlwidgets/eDISH.yaml b/inst/htmlwidgets/eDISH.yaml
@@ -4,12 +4,12 @@ dependencies:
     src: htmlwidgets/lib/d3-3.5.17
     script: d3.v3.min.js
   - name: webcharts
-    version: 1.10.0
-    src: htmlwidgets/lib/webcharts-1.10.0
+    version: 1.11.1
+    src: htmlwidgets/lib/webcharts-1.11.1
     script: webcharts.js
     stylesheet: webcharts.css
   - name: safety-eDish
-    version: 0.12.1
-    src: htmlwidgets/lib/safety-eDISH-0.12.1
-    script: safetyedish.js 
-   
+    version: 0.14.0
+    src: htmlwidgets/lib/safety-eDISH-0.14.0
+    script: safetyedish.js
+