cellbrowser 1.2.18__tar.gz → 1.2.19__tar.gz

{cellbrowser-1.2.18/src/cbPyLib/cellbrowser.egg-info → cellbrowser-1.2.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.18
+Version: 1.2.19
 Summary: UCSC Cellbrowser, an interactive browser for single cell data. Includes converters and basic pipelines for text files, Seurat, Scanpy and Cellranger.
 Home-page: https://github.com/maximilianh/cellBrowser
 Author: Maximilian Haeussler

{cellbrowser-1.2.18 → cellbrowser-1.2.19}/src/cbPyLib/cellbrowser/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-06-04T08:52:42-0700",
+ "date": "2026-06-04T15:16:16-0700",
  "dirty": true,
  "error": null,
- "full-revisionid": "c09cf26bfbea561975af659004344a386b68819f",
- "version": "1.2.18"
+ "full-revisionid": "16f80db61593316c8f6cf3def90e89d82a7946f1",
+ "version": "1.2.19"
 }
 '''  # END VERSION_JSON
 

{cellbrowser-1.2.18 → cellbrowser-1.2.19}/src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js

@@ -8976,17 +8976,18 @@ var cellbrowser = function() {
             //getById("tpGeneExprLimitApply").disabled = isDisabled;
         //});
         
-        // use the current gene
-        let geneId = getVar("gene", null);
-        
-        // if there is none, pick a reasonable default gene and meta var
-        if (geneId===null && db.conf.quickGenes)
-            geneId = db.conf.quickGenes[0][0];
-        if (geneId==null)
-            geneId = db.getRandomLocus();
-
-        // URL variables can override the defaults
-        let geneIds = getVar("exprGene", geneId).split(" ");
+        // URL variables override everything; otherwise load all quickGenes; last resort: single gene
+        let geneIds;
+        if (getVar("exprGene", null) !== null) {
+            geneIds = getVar("exprGene", null).split(" ");
+        } else if (db.conf.quickGenes && db.conf.quickGenes.length > 0) {
+            geneIds = db.conf.quickGenes.map(function(qg) { return qg[0]; });
+        } else {
+            let geneId = getVar("gene", null);
+            if (geneId === null)
+                geneId = db.getRandomLocus();
+            geneIds = [geneId];
+        }
 
         buildGeneExprPlotsAddGenes(geneIds, metaName); 
     }
@@ -11617,6 +11618,7 @@ function onClusterNameHover(clusterName, nameIdx, ev, isLegend, doScroll, intKey
         //if (acronyms!==undefined && clusterName in acronyms)
             //title += " - "+acronyms[clusterName];
         showDialogBox(htmls, title, {width: winWidth, height:winHeight, "buttons":buttons});
+        hideTooltip();
         $(".ui-widget-content").css("padding", "0");
         $("#tabs").tabs();
     }
@@ -11673,6 +11675,28 @@ function onClusterNameHover(clusterName, nameIdx, ev, isLegend, doScroll, intKey
             sortOrderNum = 1;
 
         var tableId = "tpMarkerTable-"+markerListIdx;
+
+        // Optional column reordering: build permutation from markerInfo.columnOrder
+        var symColIdx = 1; // default: symbol is at col 1
+        var reorderRow = null;
+        if (markerInfo.columnOrder) {
+            var nameToIdx = {};
+            for (var ci = 0; ci < headerRow.length; ci++)
+                nameToIdx[headerRow[ci].split("|")[0]] = ci;
+            var perm = [0]; // col 0 (id/geneId) always first
+            markerInfo.columnOrder.forEach(function(name) {
+                var idx = nameToIdx[name];
+                if (idx !== undefined && idx !== 0) perm.push(idx);
+            });
+            for (var ci = 1; ci < headerRow.length; ci++)
+                if (perm.indexOf(ci) === -1) perm.push(ci);
+            symColIdx = perm.indexOf(1);
+            reorderRow = function(row) {
+                return perm.map(function(pi) { return row[pi] !== undefined ? row[pi] : ""; });
+            };
+            headerRow = reorderRow(headerRow);
+        }
+
         //htmls.push("<table class='table' data-sortlist='[[1,1],[4,0]]' id='tpMarkerTable'>");
         htmls.push("<table class='table' data-sortlist='[["+sortColumn+","+sortOrder+"]]' id='"+tableId+"'>");
         htmls.push("<thead>");
@@ -11737,7 +11761,10 @@ function onClusterNameHover(clusterName, nameIdx, ev, isLegend, doScroll, intKey
                 htmls.push("<th"+addStr+">");
             else
                 htmls.push("<th style='width:"+width+"'"+addStr+">");
-            colLabel = colLabel.replace(/_/g, " ");
+            if (markerInfo.columnLabels && markerInfo.columnLabels[colLabel])
+                colLabel = markerInfo.columnLabels[colLabel];
+            else
+                colLabel = colLabel.replace(/_/g, " ");
             htmls.push(colLabel);
             htmls.push("</th>");
         }
@@ -11764,6 +11791,9 @@ function onClusterNameHover(clusterName, nameIdx, ev, isLegend, doScroll, intKey
             }
         }
 
+        if (reorderRow)
+            allDataRows = allDataRows.map(reorderRow);
+
         function buildRowsHtml(subset) {
             var h = [];
             for (var i = 0; i < subset.length; i++) {
@@ -11778,27 +11808,29 @@ function onClusterNameHover(clusterName, nameIdx, ev, isLegend, doScroll, intKey
                 var geneId = row[0];
                 if (geneId.indexOf("|") > -1)
                     geneId = geneId.split("|")[0];
-                var geneSym = row[1];
-                h.push("<td><a data-gene='"+geneId+"' class='link tpLoadGeneLink'>"+geneSym+"</a>");
-                if (hubUrl!==null) {
-                    var fullHubUrl = hubUrl+"&position="+geneSym+"&singleSearch=knownCanonical";
-                    h.push("<a target=_blank class='link' style='margin-left: 10px; font-size:80%; color:#AAA' title='link to UCSC Genome Browser' href='"+fullHubUrl+"'>Genome</a>");
-                }
-                h.push("</td>");
-                for (var j = 2; j < row.length; j++) {
+                var geneSym = row[symColIdx];
+                for (var j = 1; j < row.length; j++) {
                     var val = row[j];
                     h.push("<td>");
-                    if (val.startsWith("./")) {
-                        var imgUrl = val.replace("./", db.url+"/");
-                        var imgHtml = '<img width="100px" src="'+imgUrl+'">';
-                        val = "<a data-toggle='tooltip' data-placement='auto' class='tpPlots link' target=_blank title='"+imgHtml+"' href='"+ imgUrl + "'>plot</a>";
+                    if (j === symColIdx) {
+                        h.push("<a data-gene='"+geneId+"' class='link tpLoadGeneLink'>"+geneSym+"</a>");
+                        if (hubUrl!==null) {
+                            var fullHubUrl = hubUrl+"&position="+geneSym+"&singleSearch=knownCanonical";
+                            h.push("<a target=_blank class='link' style='margin-left: 10px; font-size:80%; color:#AAA' title='link to UCSC Genome Browser' href='"+fullHubUrl+"'>Genome</a>");
+                        }
+                    } else {
+                        if (val.startsWith("./")) {
+                            var imgUrl = val.replace("./", db.url+"/");
+                            var imgHtml = '<img width="100px" src="'+imgUrl+'">';
+                            val = "<a data-toggle='tooltip' data-placement='auto' class='tpPlots link' target=_blank title='"+imgHtml+"' href='"+ imgUrl + "'>plot</a>";
+                        }
+                        if (j===geneListCol || j===exprCol)
+                            geneListFormat(h, val, geneSym);
+                        else if (j===pValCol)
+                            h.push(parseFloat(val).toPrecision(5));
+                        else
+                            geneListFormat(h, val, geneSym);
                     }
-                    if (j===geneListCol || j===exprCol)
-                        geneListFormat(h, val, geneSym);
-                    else if (j===pValCol)
-                        h.push(parseFloat(val).toPrecision(5));
-                    else
-                        geneListFormat(h, val, geneSym);
                     h.push("</td>");
                 }
                 h.push("</tr>");

{cellbrowser-1.2.18 → cellbrowser-1.2.19}/src/cbPyLib/cellbrowser/cbWeb/js/maxPlot.js

@@ -1490,14 +1490,15 @@ function MaxPlot(div, top, left, width, height, args) {
            count++;
        }
 
-       // overdraw the selection as black rectangles on top
+       // overdraw the selection as black rectangles on top, at 2x radius so they stand out
        //if (fatIdx===null) {
            ctx.globalAlpha = 0.7;
            ctx.fillStyle= self.isLight() ? "black" : "white";
+           var selRadius = radius * 2, selDblSize = selRadius * 2;
             selCells.forEach(function(cellId) {
                let pxX = pxCoords[2*cellId];
                let pxY = pxCoords[2*cellId+1];
-               ctx.fillRect(pxX-radius, pxY-radius, dblSize, dblSize);
+               ctx.fillRect(pxX-selRadius, pxY-selRadius, selDblSize, selDblSize);
                count += 1;
             })
        //}
@@ -2021,21 +2022,19 @@ function MaxPlot(div, top, left, width, height, args) {
        if (origCoordColors)
             coordColors = origCoordColors;
 
-       // overdraw the selection on top: as circles with black outlines
+       // overdraw the selection on top: as circles with black outlines, scaled 2x so they stand out
        ctx.globalAlpha = 0.7;
-       var selImgIdx = templates.selImgIdx; // second-to last template is the black outline, see makeCircleTemplates()
+       var selImgIdx = templates.selImgIdx;
+       var selRadius = radius * 2;
+       var selTileSize = selRadius * 2 + 2;
        selCells.forEach(function(cellId) {
            let pxX = pxCoords[2*cellId];
            let pxY = pxCoords[2*cellId+1];
            if (isHidden(pxX, pxY))
                 return;
-           // make sure that old leftover overlapping black circles don't shine through and redraw the circle
-           // slow, but not sure what else I can do...
            let col = coordColors[cellId];
-           ctx.drawImage(off, col * tileWidth, 0, tileWidth, tileHeight, pxX - radius -1, pxY - radius-1, tileWidth, tileHeight);
-
-           // and draw the outline
-           ctx.drawImage(off, selImgIdx * tileWidth, 0, tileWidth, tileHeight, pxX - radius -1, pxY - radius-1, tileWidth, tileHeight);
+           ctx.drawImage(off, col * tileWidth, 0, tileWidth, tileHeight, pxX - selRadius - 1, pxY - selRadius - 1, selTileSize, selTileSize);
+           ctx.drawImage(off, selImgIdx * tileWidth, 0, tileWidth, tileHeight, pxX - selRadius - 1, pxY - selRadius - 1, selTileSize, selTileSize);
         });
 
        ctx.restore();
@@ -2153,8 +2152,10 @@ function MaxPlot(div, top, left, width, height, args) {
             ctx.drawArrays(self.ctx.POINTS, 0, count);
         }
         if(selCells.size > 0) {
+            ctx.uniform1f(self.u_Radius, radius * 2);
             ctx.uniform1f(self.u_Layer, 2);
             ctx.drawArrays(self.ctx.POINTS, 0, count);
+            ctx.uniform1f(self.u_Radius, radius);
         }
         if(WEBGL_DEBUG) {
             ctx.finish();
@@ -2257,17 +2258,24 @@ function MaxPlot(div, top, left, width, height, args) {
                count++;
        }
 
-       // overdraw the selection as black pixels
+       // overdraw the selection as black 3x3 blocks so they're visible at radius=0
         if (fatIdx===null) {
             selCells.forEach(function(cellId) {
                let pxX = pxCoords[2*cellId];
                let pxY = pxCoords[2*cellId+1];
                if (isHidden(pxX, pxY))
                     return;
-               let p = 4 * (pxY*width+pxX); // pointer to red value of pixel at x,y
-               cData[p] = 0;
-               cData[p+1] = 0;
-               cData[p+2] = 0;
+               for (let dy = -1; dy <= 1; dy++) {
+                   for (let dx = -1; dx <= 1; dx++) {
+                       let nx = pxX + dx, ny = pxY + dy;
+                       if (nx < 0 || nx >= width || ny < 0 || ny >= height) continue;
+                       let p = 4 * (ny*width+nx);
+                       cData[p] = 0;
+                       cData[p+1] = 0;
+                       cData[p+2] = 0;
+                       cData[p+3] = 255;
+                   }
+               }
             })
         }
 

{cellbrowser-1.2.18 → cellbrowser-1.2.19}/src/cbPyLib/cellbrowser/cellbrowser.py

@@ -4187,6 +4187,10 @@ def convertMarkers(inConf, outConf, geneToSym, clusterLabels, matrixGeneIds, out
         newDict = {"name" : sanitizeName(clusterName), "shortLabel" : markerLabel, "clusterList": list(clusterNames)}
         if "selectOnClick" in markerInfo:
             newDict["selectOnClick"] = markerInfo["selectOnClick"]
+        if "columnOrder" in markerInfo:
+            newDict["columnOrder"] = markerInfo["columnOrder"]
+        if "columnLabels" in markerInfo:
+            newDict["columnLabels"] = markerInfo["columnLabels"]
         newMarkers.append( newDict )
 
     outConf["markers"] = newMarkers

{cellbrowser-1.2.18 → cellbrowser-1.2.19/src/cbPyLib/cellbrowser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.18
+Version: 1.2.19
 Summary: UCSC Cellbrowser, an interactive browser for single cell data. Includes converters and basic pipelines for text files, Seurat, Scanpy and Cellranger.
 Home-page: https://github.com/maximilianh/cellBrowser
 Author: Maximilian Haeussler