Merge pull request #91 from Integrative-Transcriptomics/dev

Dev

Author: mwittep

src/components/Result.jsx

@@ -73,8 +73,18 @@ function Result() {
     const allRows = masterTable.trim().split("\n"); // trim() removes trailing newline
     const headers = allRows[0].split("\t");
     let IDofSelectableColumns = []
+    const isGenomeComparison = headers.indexOf("Genome") !== -1 
     let tmpMetadataColumns = {}
-    const col = headers.map((h, i) => {
+    let col = headers.map((h, i) => {
+      if (!isGenomeComparison) {
+        if (["Pos", "Strand"].includes(h)) {
+          return null;
+        }
+        if (["SuperPos", "SuperStrand"].includes(h)) {
+          // Remove "Super" prefix
+          h = h.replace("Super", "");
+        }
+      }
       if (selectHeaders.includes(h)) {
         IDofSelectableColumns.push(i)
       }
@@ -89,7 +99,8 @@ function Result() {
         sortingFn: h.startsWith("rep") ? "myReplicateSorting" : cappedValues.includes(h) ? "myCappedSorting" : sortingFns.alphanumeric
       };
     });
-    const searchFor = headers.indexOf("Genome") !== -1 ? "Genome" : "Condition";
+    col = col.filter((c) => c !== null);
+    const searchFor = isGenomeComparison ? "Genome" : "Condition";
     const genomeIdx = headers.indexOf(searchFor);
 
     const allG = new Set();

src/components/Result/GoslingVisualizations/AlignedGenomeViz.jsx

@@ -107,7 +107,7 @@ function AlignedGenomeViz({ dataGosling, filter, filePath, gosRef, maxValueWiggl
     }
     const completeView = (views, color, subtitle) => {
         return {
-            "style": { "background": color, "backgroundOpacity": 0.25, "outline": "black", "outlineWidth": 2 },
+            "style": { "backgroundOpacity": 0.25, "outline": "black", "outlineWidth": 2 },
             "subtitle": subtitle,
             "spacing": 0,
             "arrangement": "vertical",

src/components/Result/GoslingVisualizations/SharedGoslingFunctions.js

@@ -63,7 +63,7 @@ export const createGenomeTrack = (filePath, genome, strand = "+",width) => {
         "mark": "text",
         "text": { "field": "base", "type": "nominal" },
         "x": { "field": "pos", "type": "genomic" },
-        "style": { "textFontWeight": "bold", "align": "center" },
+        "style": { "textFontWeight": "bold", "align": "center" , "textAlign": "center"},
         "size": { "value": 16 },
         "color": {
             "field": "base",
@@ -77,8 +77,8 @@ export const createGenomeTrack = (filePath, genome, strand = "+",width) => {
                     {
                         "operation": "LT",
                         "measure": "zoomLevel",
-                        "threshold": 500,
-                        "transitionPadding": 1000,
+                        "threshold": 125,
+                        "transitionPadding": 50,
                         "target": "mark"
                     }]
 
@@ -110,8 +110,6 @@ export const createBinnedView = (filePath, binSize, maxValueBin, filterTSS, stra
         "xe": { "field": "binEnd", "type": "genomic", "axis": "none" },
         "mark": "bar",
         width: width,
-
-        "style": { "background": strand === "+" ? "lightblue" : "#f59f95", "backgroundOpacity": 0.25 },
         "y": {
             "field": "count",
             "type": "quantitative",
@@ -221,10 +219,9 @@ export const createGFFTrack = (filePath, genomeName, strand, width) => {
         "mark": "rect",
         "x": { "field": "start", "type": "genomic", "axis": "none" },
         "xe": { "field": "end", "type": "genomic", "axis": "none" },
-        "color": { "value": "grey" },
-        "opacity": { "value": 0.4 },
+        "color": { "value": "darkgrey" },
+        "opacity": { "value": 0.75 },
         "size": { "value": 4 },
-        "style": { background: strand === "+" ? "lightblue" : "#f59f95", backgroundOpacity: 0.15 },
         "tracks": [
             {
                 "tooltip": [

src/components/Result/GoslingVisualizations/SingleGenomeViz.jsx

@@ -38,7 +38,6 @@ function SingleGenomeViz({ dataGosling, filter, filePath, gosRef, maxValueWiggle
         return [
             {
                 "alignment": "overlay",
-                "style": { background: strand === "+" ? "lightblue" : "#f59f95", backgroundOpacity: 0.25 },
                 "tracks": [
                     detailTSSTrack,
                     ...binnedViews,
@@ -72,9 +71,7 @@ function SingleGenomeViz({ dataGosling, filter, filePath, gosRef, maxValueWiggle
         let views = [];
         for (let genome of Object.keys(data)) {
             views.push({
-                style: {
-                    background: "lightgray", backgroundOpacity: 0.25, outline: "black", outlineWidth: 2
-                },
+                style: {outline: "black", outlineWidth: 2},
                 "alignment": "stack",
                 "assembly": [[genome, data[genome]["lengthGenome"]]],
                 "spacing": 0,