diffexp performance & UX improvements (#431)

* new diffexp REST API spec

* new diffexp REST API; faster diffexp and dataframe slicing

* first draft of fast diffexp

* convert variance calculation to two-pass method

* lint

* update front-end use of API

* fix typo in spec

* disable content compression

* catch index filter format errors

* clean up of dead code

* resolve PR review comments

client/src/actions/index.js

@@ -90,12 +90,16 @@ async function _doRequestExpressionData(dispatch, getState, genes) {
   const state = getState();
   const { universe } = state.controls;
   /* preload data already in cache */
-  let expressionData = _.transform(genes, (expData, g) => {
-    const data = kvCache.get(universe.varDataCache, g);
-    if (data) {
-      expData[g] = data;
-    }
-  }); // --> { gene: data }
+  let expressionData = _.transform(
+    genes,
+    (expData, g) => {
+      const data = kvCache.get(universe.varDataCache, g);
+      if (data) {
+        expData[g] = data;
+      }
+    },
+    {}
+  ); // --> { gene: data }
   /* make a list of genes for which we do not have data */
   const genesToFetch = _.filter(genes, g => expressionData[g] === undefined);
 
@@ -119,7 +123,6 @@ async function _doRequestExpressionData(dispatch, getState, genes) {
           }),
           headers: new Headers({
             accept: "application/json",
-            "Accept-Encoding": "gzip, deflate, br",
             "Content-Type": "application/json"
           })
         }
@@ -239,7 +242,6 @@ const requestDifferentialExpression = (set1, set2, num_genes = 10) => async (
         method: "POST",
         headers: new Headers({
           Accept: "application/json",
-          "Accept-Encoding": "gzip, deflate, br",
           "Content-Type": "application/json"
         }),
         body: JSON.stringify({

client/src/components/brushableHistogram/index.js

@@ -248,9 +248,9 @@ class HistogramBrush extends React.Component {
       colorAccessor,
       isUserDefined,
       isDiffExp,
-      avgDiff,
-      set1AvgExp,
-      set2AvgExp,
+      logFoldChange,
+      pval,
+      pvalAdj,
       scatterplotXXaccessor,
       scatterplotYYaccessor,
       zebra
@@ -337,25 +337,17 @@ class HistogramBrush extends React.Component {
             }}
           >
             <span>
-              <strong>1:</strong>
-              {` ${set1AvgExp.toPrecision(2)}`}
+              <strong>log fold change:</strong>
+              {` ${logFoldChange.toPrecision(4)}`}
             </span>
             <span
               style={{
                 marginLeft: 7,
-                backgroundColor: globals.lighterGrey,
                 padding: 2
               }}
             >
-              <strong>2:</strong>
-              {` ${set2AvgExp.toPrecision(2)}`}
-            </span>
-            <span
-              style={{
-                marginLeft: 7
-              }}
-            >
-              {`Av. Diff: ${avgDiff.toFixed(2)}`}
+              <strong>p-value (adj):</strong>
+              {pvalAdj < 0.0001 ? " < 0.0001" : ` ${pvalAdj.toFixed(4)}`}
             </span>
           </div>
         ) : null}

client/src/components/geneExpression/index.js

@@ -152,9 +152,9 @@ class GeneExpression extends React.Component {
                     zebra={index % 2 === 0}
                     ranges={d3.extent(values)}
                     isDiffExp
-                    avgDiff={value[1]}
-                    set1AvgExp={value[4]}
-                    set2AvgExp={value[5]}
+                    logFoldChange={value[1]}
+                    pval={value[2]}
+                    pvalAdj={value[3]}
                   />
                 );
               })

client/src/util/actionHelpers.js

@@ -31,8 +31,7 @@ export const doJsonRequest = async url => {
   const res = await fetch(url, {
     method: "get",
     headers: new Headers({
-      "Content-Type": "application/json",
-      "Accept-Encoding": "gzip, deflate, br"
+      "Content-Type": "application/json"
     })
   });
   if (res.ok && res.headers.get("Content-Type") === "application/json") {