cellbrowser 1.2.17__tar.gz → 1.2.17.2__tar.gz

{cellbrowser-1.2.17/src/cbPyLib/cellbrowser.egg-info → cellbrowser-1.2.17.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.17
+Version: 1.2.17.2
 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-1.2.17 → cellbrowser-1.2.17.2}/src/cbPyLib/cellbrowser/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-04-22T13:09:32-0700",
+ "date": "2026-05-01T08:30:24-0700",
  "dirty": false,
  "error": null,
- "full-revisionid": "73100b2c3973b545756150bc92f27113edf0f592",
- "version": "1.2.17"
+ "full-revisionid": "1a6a9ab68b092f7e8817e346ddb0bef41da4dfbf",
+ "version": "1.2.17.2"
 }
 '''  # END VERSION_JSON
 

{cellbrowser-1.2.17 → cellbrowser-1.2.17.2}/src/cbPyLib/cellbrowser/cbWeb/js/cbData.js

@@ -238,8 +238,26 @@ var cbUtil = (function () {
                 var dec = new TextDecoder("utf-8");
                 binData = dec.decode(arr);
             }
-            else if (this._arrType!=="string")
+            else if (this._arrType!=="string") {
+                // For URLs ending in .gz (e.g. coords.bin.gz), we may receive either
+                // the raw gzip stream (typical with Apache, since .gz is not re-compressed)
+                // or auto-decompressed bytes (if the server set Content-Encoding: gzip).
+                // Detect the gzip magic header (0x1f 0x8b) to handle both cases.
+                var urlPath = this._url.split("?")[0];
+                if (urlPath.endsWith(".gz")) {
+                    var bytes = new Uint8Array(binData);
+                    if (bytes.length >= 2 && bytes[0] === 0x1f && bytes[1] === 0x8b) {
+                        // pako returns a Uint8Array that may be a view into a
+                        // larger pre-allocated pool, so .buffer can be longer
+                        // than the actual data and not a multiple of 4. Slice
+                        // out exactly the decompressed bytes into a fresh
+                        // ArrayBuffer before constructing the typed array.
+                        var ungz = pako.ungzip(bytes);
+                        binData = ungz.buffer.slice(ungz.byteOffset, ungz.byteOffset + ungz.byteLength);
+                    }
+                }
                 binData = new this._arrType(binData);
+            }
         }
 
         this._onDone(binData, this._otherInfo);
@@ -544,7 +562,10 @@ function CbDbFile(url) {
             }
         }
 
-        var binUrl = cbUtil.joinPaths([self.url, "coords", coordInfo.name, "coords.bin"]);
+        // coords.bin was renamed to coords.bin.gz in cbBuild — see coordInfo.gzip in dataset.json.
+        // Old datasets without the gzip flag continue to serve the uncompressed coords.bin.
+        var binFname = coordInfo.gzip ? "coords.bin.gz" : "coords.bin";
+        var binUrl = cbUtil.joinPaths([self.url, "coords", coordInfo.name, binFname]);
         if (coordInfo.md5)
             binUrl += "?"+coordInfo.md5;
         var arrType = cbUtil.makeType(coordInfo.type || "float64");

{cellbrowser-1.2.17 → cellbrowser-1.2.17.2}/src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js

@@ -763,12 +763,18 @@ var cellbrowser = function() {
             $( "#pane3" ).hide();
             $( "#tabLink3" ).hide();
         } else {
-            if (desc.coordFiles===undefined) {
+            if (desc.hideDownload===true || desc.hideDownload=="True" || desc.hideDownload=="true") {
+                htmls.push("The downloads section has been deactivated by the authors. Please contact the dataset authors to get access.");
+                $( "#pane3" ).html(htmls.join(""));
+                $( "#pane3" ).show();
+                $( "#tabLink3" ).show();
+            } else if (desc.coordFiles===undefined) {
                 htmls.push("To download the data for datasets in this collection: open the collection, ");
                 htmls.push("select a dataset in the list to the left, and navigate to the 'Data Download' tab. ");
                 htmls.push("This information can also be accessed while viewing a dataset by clicking the 'Info & Downloads' button.");
-            } else if (desc.hideDownload===true || desc.hideDownload=="True" || desc.hideDownload=="true") {
-                htmls.push("The downloads section has been deactivated by the authors. Please contact the dataset authors to get access.");
+                $( "#pane3" ).html(htmls.join(""));
+                $( "#pane3" ).show();
+                $( "#tabLink3" ).show();
             } else {
                 if (desc.matrices) {
                     htmls.push("<p>");
@@ -1746,7 +1752,7 @@ var cellbrowser = function() {
     function onRadiusAlphaChange(radius, alpha) {
         /* user changed alpha or radius value */
         getById("tpSizeInput").value = radius;
-        getById("tpAlphaInput").value = alpha;
+        getById("tpAlphaInput").value = 8-alpha;
     }
     function onSaveAsClick() {
     /* File - Save Image as ... */
@@ -3028,7 +3034,7 @@ var cellbrowser = function() {
         }
 
         var label = url;
-        if (url.endsWith("coords.bin"))
+        if (url.endsWith("coords.bin") || url.endsWith("coords.bin.gz"))
             label = "Loading Coordinates";
         else if (url.endsWith(".bin"))
             label = "Loading cell annotations";
@@ -3142,7 +3148,7 @@ var cellbrowser = function() {
 
        changeUrl({"pal":null});
        // clear the gene search box
-       var select = $('#tpGeneCombo')[0].selectize.clear();
+       selectizeClear('tpGeneCombo');
     }
 
     function activateTab(name) {
@@ -3424,21 +3430,28 @@ var cellbrowser = function() {
     }
 
     function selectizeSetValue(elId, name) {
-        /* little convenience method to set a selective dropdown to a given
-         * value. does not trigger the change event. */
+        /* set a gene combobox to a given value. Works for both selectize typeahead
+         * and the select2 dropdown used for small gene sets. Does not fire change. */
         if (name===undefined)
             return;
-        var sel = getById(elId).selectize;
-        sel.addOption({id: name, text: name});
-        sel.setValue(name, 1); // 1 = do not fire change
+        var el = getById(elId);
+        if (el && el.selectize) {
+            el.selectize.addOption({id: name, text: name});
+            el.selectize.setValue(name, 1); // 1 = do not fire change
+        } else {
+            // select2: change.select2 updates the UI without firing user change handlers
+            $("#"+elId).val(name).trigger("change.select2");
+        }
     }
 
     function selectizeClear(elId) {
-        /* clear a selectize Dropdown */
-        if (name===undefined)
-            return;
-        var sel = getById(elId).selectize;
-        sel.clear();
+        /* clear a gene combobox. Works for both selectize and select2. */
+        var el = getById(elId);
+        if (!el) return;
+        if (el.selectize)
+            el.selectize.clear();
+        else
+            $("#"+elId).val(null).trigger("change.select2");
     }
 
     function colorByNothing() {
@@ -4661,7 +4674,7 @@ var cellbrowser = function() {
 
     function onSetRadiusAlphaClick(ev) {
         let newRadius = parseFloat(getById('tpSizeInput').value);
-        let newAlpha = parseFloat(getById('tpAlphaInput').value);
+        let newAlpha = 8-parseFloat(getById('tpAlphaInput').value);
         renderer.setRadiusAlpha(newRadius, newAlpha);
         renderer.drawDots();
     }
@@ -6161,9 +6174,66 @@ var cellbrowser = function() {
         });
     }
 
+    function switchToHeat() {
+       /* hide the renderer and legend and put the heatmap over them */
+       renderer.div.style.display = 'none';
+       $("#tpLegendBar").hide();
+
+       var heatLeft = metaBarWidth+metaBarMargin;
+       var heatWidth = window.innerWidth - heatLeft - 3;
+       var heatTop  = menuBarHeight + toolBarHeight;
+       var heatHeight  = window.innerHeight - heatTop;
+
+       let divEl = document.createElement('div');
+       divEl.style.position = "absolute";
+       divEl.style.overflow = "scroll";
+       divEl.style.left = heatLeft+"px";
+       divEl.style.top = heatTop+"px";
+       divEl.style.width = heatWidth+"px";
+       divEl.style.height = heatHeight+"px";
+       divEl.id = "tpHeat";
+
+       document.body.appendChild(divEl);
+
+       let geneIds = [];
+       if (db.geneCount < 200)
+           geneIds = db.allGeneIds();
+       else {
+          if (db.conf.quickGenes) {
+              for (let qg of db.conf.quickGenes)
+                  geneIds.push(qg[0]);
+          }
+       }
+
+       if (!geneIds || geneIds.length===0) {
+           alert("No quick genes are defined. Heatmaps currently only work on pre-defined gene sets.");
+           return;
+       }
+
+       let metaName = getActiveColorField();
+
+       var heatmap = new MaxHeat(divEl, {mainRenderer:renderer});
+       db.heatmap = heatmap;
+       db.heatmap.exprData = null;
+
+       function onExprDataDoneHeat(exprData) {
+           plotHeatmap(divEl, metaName, exprData);
+       }
+
+       loadGroupedExprData(db.heatmap.exprData, geneIds, metaName, onExprDataDoneHeat);
+    }
+
+    function useGeneDropdown() {
+        /* Use a searchable dropdown (all genes pre-populated) rather than a
+         * typeahead, when the gene list is small enough to fit comfortably. */
+        if (db.conf.atacSearch) return false;
+        return db.geneCount && db.geneCount <= 300;
+    }
+
+
     function activateGeneCombo(id, onGeneComboChange) {
-    /* initialize the gene search combo box with selectize */
-        // selectize: gene or ATAC Color by search box
+    /* initialize the gene search combo box. Uses a select2 dropdown with all
+     * options pre-populated for small gene sets; selectize typeahead otherwise. */
         var comboLoad = comboLoadGene;
         if (db.conf.atacSearch) {
             comboLoad = comboLoadAtac;
@@ -6174,6 +6244,32 @@ var cellbrowser = function() {
 
         }
 
+        if (useGeneDropdown()) {
+            var selectEl = getById(id);
+            var geneIds = db.allGeneIds();
+            var opts = [];
+            for (var i=0; i<geneIds.length; i++)
+                opts.push(db.getGeneInfo(geneIds[i]));
+            opts.sort(function(a, b) { return a.sym.localeCompare(b.sym); });
+            var placeholder = selectEl.getAttribute("placeholder") || "";
+            // select2 needs an empty <option> first to show the placeholder
+            var html = ['<option></option>'];
+            for (var j=0; j<opts.length; j++) {
+                var text = opts[j].sym;
+                if (opts[j].sym !== opts[j].id)
+                    text = opts[j].sym + " (" + opts[j].id + ")";
+                html.push('<option value="'+opts[j].id+'">'+text+'</option>');
+            }
+            selectEl.innerHTML = html.join("");
+            var widthPx = selectEl.style.width || 'resolve';
+            $("#"+id).select2({
+                placeholder: placeholder,
+                allowClear: true,
+                width: widthPx
+            }).on("change", onGeneComboChange);
+            return;
+        }
+
         var select = $("#"+id).selectize({
                 maxItems: 1,
                 valueField : 'id',
@@ -7495,7 +7591,7 @@ var cellbrowser = function() {
         htmls.push("<ul>");
         htmls.push("<li><a href='#tpAnnotTab'>Annotation</a></li>");
         htmls.push("<li><a href='#tpGeneTab'>"+getGeneLabel()+"</a></li>");
-        htmls.push("<li><a href='#tpLayoutTab'>Layout</a></li>");
+        htmls.push("<li><a href='#tpLayoutTab'>"+(db.conf.coordLabel || "Layout")+"</a></li>");
         htmls.push("</ul>");
 
         htmls.push("<div id='tpAnnotTab'>");
@@ -7889,7 +7985,12 @@ var cellbrowser = function() {
         Mousetrap.bind('m', function() {$('#tpMetaCombo').trigger("chosen:open"); return false;});
         Mousetrap.bind('d', function() {$('#tpDatasetCombo').trigger("chosen:open"); return false;});
         //Mousetrap.bind('l', function() {$('#tpLayoutCombo').trigger("chosen:open"); return false;});
-        Mousetrap.bind('g', function() {$("#tpGeneCombo").selectize()[0].selectize.focus(); return false;});
+        Mousetrap.bind('g', function() {
+            var el = getById("tpGeneCombo");
+            if (el && el.selectize) el.selectize.focus();
+            else $("#tpGeneCombo").select2('open');
+            return false;
+        });
         Mousetrap.bind('c l', onHideShowLabelsClick );
         Mousetrap.bind('f c', onFindCellsClick );
         Mousetrap.bind('f i', function() { onSelectByIdClick(); return false; } );

{cellbrowser-1.2.17 → cellbrowser-1.2.17.2}/src/cbPyLib/cellbrowser/cbWeb/js/maxPlot.js

@@ -439,13 +439,13 @@ function MaxPlot(div, top, left, width, height, args) {
         console.log("alpha: "+ui.value);
         var sliderVal = ui.value; // 1-7
         var multMap = {
-            7 : 0.15,
-            6 : 0.4,
-            5 : 0.8,
+            7 : 0.10,
+            6 : 0.3,
+            5 : 0.7,
             4 : 1.0,
             3 : 1.2,
             2 : 1.5,
-            1 : 1.8
+            1 : 2.0
         }
         self.port.alphaMult = multMap[sliderVal];
         console.log("alphaMult: "+self.port.alphaMult);
@@ -462,8 +462,8 @@ function MaxPlot(div, top, left, width, height, args) {
             3 : 1/1.5,
             4 : 1.0,
             5 : 1.5,
-            6 : 2.0,
-            7 : 3.0
+            6 : 2.5,
+            7 : 5.0
         }
         self.port.radiusMult = multMap[sliderVal];
         self.calcRadius();
@@ -3247,7 +3247,18 @@ function MaxPlot(div, top, left, width, height, args) {
             var x = coords[i * 2];
             var y = coords[i * 2 + 1];
 
-            if (isHidden(x, y))
+            // Skip hidden cells. HIDCOORD is the sentinel cbBuild writes for
+            // cells that have no coordinate in this layout (common in spatial
+            // datasets where each layout shows one slide). Non-WebGL also uses
+            // it for user-hidden cells; WebGL tracks user-hide separately in
+            // coords.hidden[i]. We don't use isHidden() because its WebGL
+            // branch does a viewport-bounds check in clip space, but coords
+            // here are in data space — that check would drop almost everything
+            // and labels would collapse to the canvas center. Labels follow
+            // the data, not the current zoom/pan.
+            if (x === HIDCOORD && y === HIDCOORD)
+                continue;
+            if (self.usesWebGL() && self.coords.hidden && self.coords.hidden[i] === 1)
                 continue;
 
             calc[label][0].push(x);

{cellbrowser-1.2.17 → cellbrowser-1.2.17.2}/src/cbPyLib/cellbrowser/cellbrowser.py

@@ -2678,9 +2678,17 @@ def writeCoords(coordName, coords, sampleNames, coordBinFname, coordInfo, textOu
         debugFh.close()
         logging.info("DEBUG: wrote %s" % debugFh.name)
     renameFile(tmpFname, coordBinFname)
-    
-    md5 = md5WithPython(coordBinFname)
+
+    # gzip coords.bin -> coords.bin.gz. Named .gz so Apache mod_deflate doesn't try to
+    # re-compress it on the wire. The JS reader (cbData.js) ungzips with pako.
+    # Compresses well on datasets with many hidden cells (long HIDDENCOORD runs).
+    coordBinGz = runGzip(coordBinFname)
+    if isfile(coordBinFname):
+        os.remove(coordBinFname)
+
+    md5 = md5WithPython(coordBinGz)
     coordInfo["md5"] = md5[:MD5LEN]
+    coordInfo["gzip"] = True
 
     coordInfo["minX"] = minX
     coordInfo["maxX"] = maxX
@@ -6415,6 +6423,7 @@ def makeIndexHtml(baseDir, outDir, devMode=False):
         "ext/OverlayScrollbars.min.css", # 1.6.2, from https://cdnjs.com/libraries/overlayscrollbars
         #"ext/theme.default.css", #  tablesorter
         "ext/theme.bootstrap_3.css", #  tablesorter
+        "ext/jquery.tablesorter.pager.css", # tablesorter pager addon
         "css/cellBrowser.css"
         ]
 
@@ -6440,6 +6449,7 @@ def makeIndexHtml(baseDir, outDir, devMode=False):
         "ext/jquery.event.drag-2.3.0.js", # for slickgrid 2.4.5
         "ext/jquery.tablesorter.js",
         "ext/jquery.tablesorter.widgets.js",
+        "ext/jquery.tablesorter.pager.js",
         "ext/lz-string.js",  # 1.4.4, https://raw.githubusercontent.com/pieroxy/lz-string/master/libs/lz-string.js
         "ext/slick.core.js",
         "ext/slick.cellrangedecorator.js", "ext/slick.cellrangeselector.js", "ext/slick.cellselectionmodel.js",

{cellbrowser-1.2.17 → cellbrowser-1.2.17.2}/src/cbPyLib/cellbrowser/sampleConfig/cellbrowser.conf

@@ -72,6 +72,15 @@ coords=[
     },
 ]
 
+# The "Layout" tab can be renamed, e.g. for spatial datasets
+# coordLabel="Spatial Slides"
+#
+# rarely needed: the "Genes" tab can be renamed.
+# you if your expression matrix does not contain genes, but something
+# else, like "lipids" or "plankton", you can replace the word "gene" in the
+# user interface with another word
+# geneLabel = "Lipid"
+
 # if you use the lineFile option, you can tweak their display a little with these statements, defaults are dark-grey, 0.5 and 3
 #lineColor="#112233"
 #lineAlpha=0.3
@@ -171,10 +180,6 @@ unit = "TPM"
 # or the matrix has only integers expressed like 100.000, 200.000, 300.00, ...
 matrixType='auto'
 
-# rarely needed: if your expression matrix does not contain genes, but something
-# else, like "lipids" or "plankton", you can replace the word "gene" in the
-# user interface with another word
-# geneLabel = "Lipid"
 
 # the default color palettes for this dataset. By default, we use Paul Tol's
 # but you could use other ones. change the palette in the UI, look at the URL, the value for the palette

{cellbrowser-1.2.17 → cellbrowser-1.2.17.2/src/cbPyLib/cellbrowser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.17
+Version: 1.2.17.2
 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