fix RhoInc#84; fix RhoInc#85; fix RhoInc#86

samussiah · Mar 22, 2021 · 1e1d04e · 1e1d04e
1 parent f7ac1ab
commit 1e1d04e
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Showing 14 changed files with 412 additions and 639 deletions.
diff --git a/safetyShiftPlot.js b/safetyShiftPlot.js
diff --git a/src/callbacks/onInit.js b/src/callbacks/onInit.js
@@ -26,19 +26,22 @@ export default function onInit() {
     // 4. Update control inputs.
     updateControlInputs.call(this);
 
-    //Set initial measure.
-    this.config.measure = this.config.measure || this.measures[0];
-
     //Set baseline and comparison visits.
     this.config.x_params.visits = this.config.x_params.visits || [this.visits[0]];
     this.config.y_params.visits = this.config.y_params.visits || this.visits.slice(1);
 
     //Filter raw data on initial measure and derive baseline/comparison data.
     this.measureData = this.initial_data.filter(
-        d => d[this.config.measure_col] === this.config.measure
+        d => d.ssp_measure === this.config.measure
     );
     this.filteredData = this.measureData; // filtered data placeholder
-    this.raw_data = preprocessData.call(this, this.measureData); // preprocessed measure data
+    if (Array.isArray(this.config.filters) && this.config.filters.length)
+        this.config.filters.forEach(filter => {
+            if (filter.start)
+                this.filteredData = this.filteredData
+                    .filter(d => d[filter.value_col] === filter.start);
+        });
+    this.raw_data = preprocessData.call(this, this.filteredData); // preprocessed measure data
 
     //Define initial domains.
     this.config.x.domain = extent(this.raw_data.map(d => d.shiftx));

diff --git a/src/callbacks/onInit/addVariables.js b/src/callbacks/onInit/addVariables.js
@@ -1,5 +1,8 @@
 export default function addVariables() {
     this.initial_data.forEach(d => {
         d[this.config.measure_col] = d[this.config.measure_col].trim();
+        d.ssp_measure = d.hasOwnProperty(this.config.unit_col)
+            ? `${d[this.config.measure_col]} (${d[this.config.unit_col]})`
+            : d[this.config.measure_col];
     });
 }
diff --git a/src/callbacks/onInit/getMeasures.js b/src/callbacks/onInit/getMeasures.js
@@ -1,7 +1,30 @@
-import { set } from 'd3';
+import { dataOps } from 'webcharts';
 
 export default function getMeasures() {
-    this.measures = set(this.initial_data.map(d => d[this.config.measure_col]))
-        .values()
-        .sort();
+    // Define set of measure values as they appear in the data.
+    this.measures = this.initial_data[0].hasOwnProperty(this.config.measure_order_col)
+        ? [...new Set(this.initial_data.map(d => +d[this.config.measure_order_col])).values()]
+              .sort((a, b) => a - b)
+              .map(
+                  value =>
+                      this.initial_data.find(d => +d[this.config.measure_order_col] === value)[
+                          this.config.measure_col
+                      ]
+              )
+        : [...new Set(this.initial_data.map(d => d[this.config.measure_col])).values()].sort(
+              dataOps.naturalSorter
+          );
+
+    // Define set of measure values with units (in ADaM units are already attached; in SDTM units are captured in a separate variable).
+    this.ssp_measures = this.initial_data[0].hasOwnProperty(this.config.measure_order_col)
+        ? [...new Set(this.initial_data.map(d => +d[this.config.measure_order_col])).values()]
+              .sort((a, b) => a - b)
+              .map(
+                  value =>
+                      this.initial_data.find(d => +d[this.config.measure_order_col] === value)
+                          .ssp_measure
+              ) // sort measures by measure order
+        : [...new Set(this.initial_data.map(d => d.ssp_measure)).values()].sort(
+              dataOps.naturalSorter
+          ); // sort measures alphabetically
 }
diff --git a/src/callbacks/onInit/updateControlInputs.js b/src/callbacks/onInit/updateControlInputs.js
@@ -1,5 +1,26 @@
 export default function updateControlInputs() {
-    this.controls.config.inputs.find(input => input.option === 'measure').values = this.measures;
+    const measureInput = this.controls.config.inputs
+        .find(input => input.option === 'measure');
+    measureInput.values = this.ssp_measures;
+    console.log(this.config.start_value);
+
+    if (
+        this.config.start_value &&
+        this.ssp_measures.indexOf(this.config.start_value) < 0 &&
+        this.measures.indexOf(this.config.start_value) < 0
+    ) {
+        measureInput.start = this.ssp_measures[0];
+        console.warn(
+            `${this.config.start_value} is an invalid measure. Defaulting to ${measureInput.start}.`
+        );
+    } else if (this.config.start_value && this.ssp_measures.indexOf(this.config.start_value) < 0) {
+        measureInput.start = this.ssp_measures[this.measures.indexOf(this.config.start_value)];
+        console.warn(
+            `${this.config.start_value} is missing the units value. Defaulting to ${measureInput.start}.`
+        );
+    } else measureInput.start = this.config.start_value || this.ssp_measures[0];
+    this.config.measure = measureInput.start;
+
     this.controls.config.inputs.find(
         input => input.option === 'x_params_visits'
     ).values = this.visits;

diff --git a/src/callbacks/onLayout/addFilters.js b/src/callbacks/onLayout/addFilters.js
@@ -5,7 +5,7 @@ export default function addFilters(chart) {
     chart.config.filters.forEach(filter => {
         //Capture distinct [filter.value_col] values.
         filter.values = set(chart.initial_data.map(d => d[filter.value_col])).values();
-        filter.value = 'All';
+        filter.value = filter.start || 'All';
 
         //Attach filter to the DOM.
         const controlGroup = chart.controls.wrap
@@ -21,9 +21,14 @@ export default function addFilters(chart) {
         //Attach distinct [filter.value_col] values as select options.
         changer
             .selectAll('option')
-            .data(['All'].concat(filter.values))
+            .data(
+                filter.all
+                    ? ['All'].concat(filter.values)
+                    : filter.values
+            )
             .enter()
             .append('option')
+            .property('selected', d => d === filter.value)
             .text(d => d);
 
         //Define dropdown event listener.

diff --git a/src/callbacks/onLayout/customizeMeasureControl.js b/src/callbacks/onLayout/customizeMeasureControl.js
@@ -11,7 +11,7 @@ export default function custmoizeMeasureControl() {
 
         //Redefine raw and preprocessed measure data, x-domain, and y-domain.
         this.measureData = this.initial_data.filter(
-            d => d[this.config.measure_col] === this.config.measure
+            d => d.ssp_measure === this.config.measure
         );
         this.raw_data = preprocessData.call(this, this.measureData);
         this.config.x.domain = extent(this.raw_data.map(d => d.shiftx));

diff --git a/src/callbacks/onResize/listVisits.js b/src/callbacks/onResize/listVisits.js
@@ -3,7 +3,7 @@ import { set } from 'd3';
 export default function listVisits() {
     var possibleVisits = set(
         this.initial_data
-            .filter(f => f[this.config.measure_col] === this.config.measure)
+            .filter(f => f.ssp_measure === this.config.measure)
             .map(d => d[this.config.visit_col])
     ).values();
     possibleVisits.sort((a, b) => this.visits.indexOf(a) - this.visits.indexOf(b));

diff --git a/src/configuration/controlInputs.js b/src/configuration/controlInputs.js
@@ -10,15 +10,15 @@ export default function controlInputs() {
         {
             type: 'dropdown',
             values: [],
-            label: 'Baseline visit(s)',
+            label: 'Timepoint 1',
             option: 'x_params_visits',
             require: true,
             multiple: true
         },
         {
             type: 'dropdown',
             values: [],
-            label: 'Comparison visit(s)',
+            label: 'Timepoint 2',
             option: 'y_params_visits',
             require: true,
             multiple: true

diff --git a/src/configuration/rendererSettings.js b/src/configuration/rendererSettings.js
@@ -5,7 +5,9 @@ export default function rendererSettings() {
         visit_col: 'VISIT',
         visit_order_col: 'VISITNUM',
         measure_col: 'TEST',
+        measure_order_col: 'TESTN',
         value_col: 'STRESN',
+        unit_col: 'STRESU',
         start_value: null,
         x_params: { visits: null, stat: 'mean' },
         y_params: { visits: null, stat: 'mean' },

diff --git a/src/configuration/syncControlInputs.js b/src/configuration/syncControlInputs.js
@@ -7,6 +7,12 @@ export default function syncControlInputs(controlInputs, settings) {
             };
             filterObject.label = filter.label || filterObject.value_col;
             filterObject.type = 'subsetter';
+            filterObject.all = filterObject.all !== undefined
+                ? filterObject.all
+                : true;
+            filterObject.start = filterObject.start !== undefined
+                ? filterObject.start
+                : null;
 
             if (filter instanceof Object) Object.assign(filterObject, filter);
 

diff --git a/src/configuration/syncSettings.js b/src/configuration/syncSettings.js
@@ -1,4 +1,3 @@
 export default function syncSettings(settings) {
-    settings.measure = settings.start_value;
     return settings;
 }
diff --git a/src/util/preprocessData.js b/src/util/preprocessData.js
@@ -11,7 +11,7 @@ export default function preprocessData(rawData) {
             return d[config.visit_col];
         })
         .key(function(d) {
-            return d[config.measure_col];
+            return d.ssp_measure;
         })
         .rollup(function(r) {
             var value = r[0][config.value_col];
@@ -24,7 +24,6 @@ export default function preprocessData(rawData) {
     }
 
     function setVal(e, params) {
-        console.log(params);
         var visits = e.values.filter(function(f) {
             return params.visits.indexOf(f.key) !== -1;
         });

diff --git a/test-page/index.js b/test-page/index.js
@@ -1,14 +1,28 @@
 d3.csv(
     'https://raw.githubusercontent.com/RhoInc/data-library/master/data/clinical-trials/renderer-specific/adbds.csv',
-    function(d) {
+    function(d,i) {
         return d;
     },
     function(data) {
-        const ssp = safetyShiftPlot(
+        const measures = [...new Set(data.map(d => d.TEST)).values()]
+            .sort(webCharts.dataOps.naturalSorter)
+            .sort(() => .5 - Math.random());
+        data.forEach(d => {
+            d.TESTN = measures.findIndex(measure => measure === d.TEST);
+        });
+
+        const instance = safetyShiftPlot(
             '#container', // element
             {
+                filters: [
+                    {value_col: 'SITEID', label: 'Site ID'},
+                    {value_col: 'SEX', label: 'Sex'},
+                    {value_col: 'RACE', label: 'Race'},
+                    {value_col: 'ARM', label: 'Treatment Group'},
+                    {value_col: 'USUBJID', label: 'Participant ID'},
+                ],
             } // settings
         );
-        ssp.init(data);
+        instance.init(data);
     }
 );