Revise based on Kevin's review

web4bio · Oct 22, 2024 · 99ea087 · 99ea087
1 parent e204341
commit 99ea087
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Showing 4 changed files with 21 additions and 28 deletions.
diff --git a/main/js/afterSubmit.js b/main/js/afterSubmit.js
@@ -205,7 +205,7 @@ const buildViolinPlot = function(geneQuery, expressionData) {
 
   meme.appendChild(numCohortBarcodes2);
 
-  let displayNumberSamplesInCohort2 = function () {
+  let displayNumberSamplesInCohort = function () {
       let existingPara = document.getElementById("numSamplesInCohortText2");
       if (existingPara) {
           existingPara.remove();
@@ -222,7 +222,7 @@ const buildViolinPlot = function(geneQuery, expressionData) {
       numCohortBarcodes2.appendChild(para);
   };
 
-  displayNumberSamplesInCohort2()
+  displayNumberSamplesInCohort()
 
   ///////////////////////////////////
 

diff --git a/main/js/fillSelectBoxes.js b/main/js/fillSelectBoxes.js
@@ -12,19 +12,19 @@
  * @returns {undefined}
  */
 const fillCancerTypeSelectBox = async function () {
-  const cancerTypesQuery_1 = await firebrowse.fetchCohorts();
-  const cancerTypesQuery = cancerTypesQuery_1.reduce((acc, item) => item.cohort !== 'FPPP' ? [...acc, item] : acc, []);
-  cancerTypesQuery.sort();
+  const cancerTypesQuery = await firebrowse.fetchCohorts();
+  const cancerTypesQueryNoFPPP = cancerTypesQuery.reduce((acc, item) => item.cohort !== 'FPPP' ? [...acc, item] : acc, []);
+  cancerTypesQueryNoFPPP.sort();
   let selectBox = document.getElementById("cancerTypeMultipleSelection");
-  for (let i = 0; i < cancerTypesQuery.length; i++) {
+  for (let i = 0; i < cancerTypesQueryNoFPPP.length; i++) {
     let currentOption = document.createElement("option");
-    currentOption.value = cancerTypesQuery[i]["cohort"];
+    currentOption.value = cancerTypesQueryNoFPPP[i]["cohort"];
     currentOption.text =
       "(" +
-      cancerTypesQuery[i]["cohort"] +
+      cancerTypesQueryNoFPPP[i]["cohort"] +
       ") " +
-      cancerTypesQuery[i]["description"];
-    currentOption.id = cancerTypesQuery[i]["cohort"];
+      cancerTypesQueryNoFPPP[i]["description"];
+    currentOption.id = cancerTypesQueryNoFPPP[i]["cohort"];
     selectBox.appendChild(currentOption);
   }
   let cancerTypeSelectedOptions = localStorage
@@ -89,29 +89,29 @@ let displayNumberSamples = async function () {
     };
     orderedCountQuery = orderThings(formatted_numbersOfSamples, myCohort, 'cohort')
     // build label:
-    let string = "";
+    let numSamplesLabel = "";
     let para;
     for (let i = 0; i < orderedCountQuery.length; i++) {
-      if (string == "") {
-        string += orderedCountQuery[i].cohort + ": " + orderedCountQuery[i].mrnaseq;
+      if (numSamplesLabel == "") {
+        numSamplesLabel += orderedCountQuery[i].cohort + ": " + orderedCountQuery[i].mrnaseq;
         para = document.createElement("P");
         para.setAttribute(
           "style",
           'text-align: center; color: #4db6ac; font-family: Georgia, "Times New Roman", Times, serif'
         );
         para.setAttribute("id", "numSamplesText");
-        para.innerText = "Number of samples: " + string;
+        para.innerText = "Number of samples: " + numSamplesLabel;
         cancerQuerySelectBox.appendChild(para);
       } else {
         document.getElementById("numSamplesText").remove();
-        string += ", " + orderedCountQuery[i].cohort +
+        numSamplesLabel += ", " + orderedCountQuery[i].cohort +
                  ": " + orderedCountQuery[i].mrnaseq;
         para.setAttribute(
           "style",
           'text-align: center; color: #4db6ac; font-family: Georgia, "Times New Roman", Times, serif'
         );
         para.setAttribute("id", "numSamplesText");
-        para.innerText = "Number of samples: " + string;
+        para.innerText = "Number of samples: " + numSamplesLabel;
         cancerQuerySelectBox.appendChild(para);
       }
     }
@@ -303,7 +303,6 @@ let fillClinicalSelectBox = async function () {
     const unwantedKeys = new Set(['date', 'tcga_participant_barcode', 'tool']);
     clinicalKeys[0] = clinicalKeys[0].filter(item => !unwantedKeys.has(item));
 
-
     let intersectedFeatures;
     if(clinicalKeys.length > 1)
       for(let i = 0; i < clinicalKeys.length - 1; i++) {
@@ -335,7 +334,7 @@ let fillClinicalSelectBox = async function () {
       let temp = {name: currentFeature, type: "", isSelected: false};
 
       let checkIfClinicalFeatureArrayIsNumeric = async function() {
-        let continuousFeaturesArr = [
+        const CONTINUOUS_FEATURES = [
           "age_began_smoking_in_years",
           "age_at_diagnosis",
           "cervix_suv_results",
@@ -367,7 +366,7 @@ let fillClinicalSelectBox = async function () {
           "years_to_birth",
           "year_of_tobacco_smoking_onset"
         ]; // Array of features that should be considered continuous
-        if(continuousFeaturesArr.includes(currentFeature))
+        if(CONTINUOUS_FEATURES.includes(currentFeature))
           temp.type = "continuous";
         else
           temp.type = "categorical";

diff --git a/main/js/plots/createHeatmap.js b/main/js/plots/createHeatmap.js
@@ -29,16 +29,16 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d
             existingPara.remove();
         }
         // build label:
-        let string = "";
+        let numSamplesLabel = "";
         let para;
-        string = (d3.map(expressionData, d => d.tcga_participant_barcode).keys()).length
+        numSamplesLabel = (d3.map(expressionData, d => d.tcga_participant_barcode).keys()).length
         para = document.createElement("P");
         para.setAttribute(
             "style",
             'text-align: center; color: #4db6ac; font-family: Georgia, "Times New Roman", Times, serif'
         );
         para.setAttribute("id", "numSamplesInCohortText");
-        para.innerText = "Number of samples in cohort: " + string;
+        para.innerText = "Number of samples in cohort: " + numSamplesLabel;
         numCohortBarcodesElement.appendChild(para);
     };
 
@@ -58,7 +58,6 @@ const createHeatmap = async function (expressionData, clinicalAndMutationData, d
     div_optionsPanels.attr("class", "col s3");
     div_optionsPanels.style("margin-top", "30px");
     div_optionsPanels.style("padding-left", "30px");
-    // div_optionsPanels.style("margin-left", "20px");
     var div_clinSelect = div_optionsPanels.append('div');
     div_clinSelect.attr("id", "heatmapPartitionSelector");
     div_clinSelect.append('text')

diff --git a/main/js/plots/createViolinPlot.js b/main/js/plots/createViolinPlot.js
@@ -211,11 +211,6 @@ const createViolinPlot = async function(dataInput, violinDiv, curPlot, facetByFi
         .call(wrap, x.bandwidth())
         .style("font-size", "8px");
 
-    // svgObject.append("text")
-    //     .attr("transform", "translate(" + width/2 + ", " + (height + margin.top + 50) + ")")
-    //     .text("Cohort")
-    //     .style("font-size", "12px");
-
     /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     /////////////////////////////////////////////////// Build the Axis and Color Scales Above ///////////////////////////////////////////////////