cellbrowser 1.2.5__tar.gz → 1.2.7__tar.gz

{cellbrowser-1.2.5/src/cbPyLib/cellbrowser.egg-info → cellbrowser-1.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.5
+Version: 1.2.7
 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-1.2.5 → cellbrowser-1.2.7}/README.rst

@@ -46,6 +46,7 @@ Many labs host their data at cells.ucsc.edu by sending it to us, but some groups
 * Lako Lab at Newcastle University, UK: http://retinalstemcellresearch.co.uk/CorneaCellAtlas/ from `Collins et al. 2021. The Ocular Surface. <https://www.sciencedirect.com/science/article/pii/S1542012421000215>`_
 * RNA Bioscience Initiative: https://www.pneuroonccellatlas.org/ and https://github.com/rnabioco/lung-scrna
 * Paul Gontarz, WUSTL, http://regmedsrv1.wustl.edu/Public_SPACE/pgontarz/Public_html/cellbrower/Exp1/
+* Dylan Farnsworth, U Oregon, https://pages.uoregon.edu/drf/browser/lens_230620/
 
 
 These papers have cell browsers made at UCSC:

{cellbrowser-1.2.5 → cellbrowser-1.2.7}/src/cbPyLib/cellbrowser/R/cellbrowser.R

@@ -232,42 +232,43 @@ ExportToCellbrowser <- function(
   reducNames <- reductions
 
   # Use or find the default cluster field
+  #if (is.null(x = cluster.field)) {
+    ## find and use the default Idents() field as the cluster field
+    #idents <- Idents(object)
+    #for (colName in colnames(object@meta.data)) {
+        #col = object@meta.data[[colName]]
+        #if (identical(idents@.Data,col@.Data)) {
+            #message("Default Idents() meta field:",colName) 
+            #cluster.field <- colName
+            #break
+        #}
+    #}
   if (is.null(x = cluster.field)) {
-    # find and use the default Idents() field as the cluster field
-    idents <- Idents(object)
-    for (colName in colnames(object@meta.data)) {
-        col = object@meta.data[[colName]]
-        if (identical(idents@.Data,col@.Data)) {
-            message("Default Idents() meta field:",colName) 
-            cluster.field <- colName
-            break
-        }
-    }
-    if (is.null(x = cluster.field)) {
-        message("There is no meta field identical to idents(): using the value of Idents() as a new field 'Cluster'")
+        message("No cluster field specified: Using the value of Idents()")
         # create a new meta data field named "Cluster"
-        newDf <- cbind(object@meta.data, Idents(object))
+        #newDf <- cbind(object@meta.data, Idents(object))
         # default name is "Idents(object)", not good, let's rename that to "Cluster"
-        names(newDf)[length(newDf)] <- "Cluster"
-        object@meta.data <- newDf
-        cluster.field <- "Cluster"
-    }
-
+        #names(newDf)[length(newDf)] <- "Cluster"
+        #object@meta.data <- newDf
+        #cluster.field <- "Cluster"
   } else {
-    message("A custom cluster field was specified: ", cluster.field)
-    Idents(object) <- as.factor(object[[cluster.field]])
+      message("A custom cluster field was specified: ", cluster.field)
+      Idents(object = object) <- cluster.field
+      # another, convoluted way to set the Idents field, if the command above makes trouble again
+      #Idents(object) <- as.factor([object[[cluster.field]], cluster.field])
   }
 
   # make sure that we have a cluster field
-  if (is.null(x = cluster.field))
-      stop("There was no cluster field provided and the auto-detection to find one based on Idents() did not work. Please provide a cluster field with cluster.field='xxx' from R or --clusterField=xxx if using cbImportSeurat. Possible meta annotation fields are: ", toString(colnames(x = meta)))
+  #if (is.null(x = cluster.field))
+      #stop("There was no cluster field provided and the auto-detection to find one based on Idents() did not work. Please provide a cluster field with cluster.field='xxx' from R or --clusterField=xxx if using cbImportSeurat. Possible meta annotation fields are: ", toString(colnames(x = meta)))
 
   if (is.null(x = meta.fields)) {
     meta.fields <- colnames(x = meta)
-    if (length(x = levels(x = Idents(object))) > 1) {
-      meta.fields <- c(meta.fields, ".ident")
-    }
+    #if (length(x = levels(x = Idents(object))) > 1) {
+      #meta.fields <- c(meta.fields, ".ident")
+    #}
   }
+
   if (!is.null(x = port) && is.null(x = cb.dir)) {
     stop("cb.dir parameter is needed when port is set")
   }

{cellbrowser-1.2.5 → cellbrowser-1.2.7}/src/cbPyLib/cellbrowser/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-02-16T09:50:21-0800",
+ "date": "2024-07-02T12:15:16-0700",
  "dirty": false,
  "error": null,
- "full-revisionid": "a1977374ebcf8f3d8c2f618ed1a6b19ef9fdf7e6",
- "version": "v1.2.5"
+ "full-revisionid": "bff421579e0abe0bc03a1f7fcc7d405155ca6d8f",
+ "version": "v1.2.7"
 }
 '''  # END VERSION_JSON
 

{cellbrowser-1.2.5 → cellbrowser-1.2.7}/src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css

@@ -178,7 +178,12 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 }
 
 /* modify bootstrap tooltip defaults */
-.tooltip-inner { min-width: 220px; border-radius: 0; background-opacity: 50%}
+.tooltip .tooltip-inner { 
+        min-width: 220px; 
+        border-radius: 0; 
+        background-opacity: 50%;
+        text-align: left
+}
 
  .ui-widget-header { background: white} 
 .ui-state-active { background: green }

{cellbrowser-1.2.5 → cellbrowser-1.2.7}/src/cbPyLib/cellbrowser/cbWeb/js/cbData.js

@@ -196,9 +196,13 @@ var cbUtil = (function () {
             if (!dataLen)
                 dataLen = new Blob([binData]).size;;
 
-            if (dataLen < expLength -1) // Yes, the -1 does not make sense. This happens only with https://cells-beta.gi.ucsc.edu/?ds=engraftable-hsc+adt
+            if (dataLen < expLength-1) // Yes, the -1 does not make sense. 
+                // This happens only with https://cells-beta.gi.ucsc.edu/?ds=engraftable-hsc+adt
                 // and I have no idea why.
-                alert("internal error cbData.js: chunk is too small. Does the HTTP server really support byte range requests?");
+                alert("internal error cbData.js: data received from web server is too short. Expected data size was "+exprLength+
+                        " but received "+dataLen+" bytes. URL: "+url+
+                        "Does the HTTP server really support byte range requests? You probably will have to contact us to "+
+                        " narrow down this problem.");
 
             if (dataLen > expLength) {
                 console.log("Webserver does not support byte range requests, working around it, but this may be slow");
@@ -356,8 +360,14 @@ var cbUtil = (function () {
         return [min, max]
     }
 
+    my.baReadBigOffset = function(ba, o) {
+    /* given a byte array, return the unsigned long long int (little endian), so eight bytes, at offset o */
+        var offset = ba[o] |  ba[o+1] << 8 | ba[o+2] << 16 | ba[o+3] << 24 | ba[o+4] << 32 | ba[o+5] << 40 | ba[o+6] << 48 | ba[o+7] << 56;
+        return offset;
+    };
+
     my.baReadOffset = function(ba, o) {
-    /* given a byte array, return the long int (little endian) at offset o */
+    /* given a byte array, return the unsigned long int (little endian), so four bytes, at offset o */
         var offset = ba[o] |  ba[o+1] << 8 | ba[o+2] << 16 | ba[o+3] << 24;
         return offset;
     };
@@ -384,7 +394,7 @@ function CbDbFile(url) {
     self.name = url;
     self.url = url;
 
-    self.exprBinCount = 25;
+    self.exprBinCount = 10;
 
     // for quick gene name searching
     self.geneSyns = null; // array of [geneSynonymLowercase, geneId]
@@ -526,6 +536,16 @@ function CbDbFile(url) {
         cbUtil.loadJson(jsonUrl, jsonDone, true);
     };
 
+    this.loadTraces = function(onTracesDone) {
+        /* load the trace file, add to self.traces and call onDone */
+        function onFileDone(res) {
+            self.traces = res;
+            onTracesDone(self.traces);
+        }
+        var fileUrl = cbUtil.joinPaths([self.url, "traces.json"]);
+        cbUtil.loadJson(fileUrl, onFileDone, true);
+    };
+
     this.getDefaultColorField = function() {
         /* return a pair: [0] is "meta" or "gene" and [1] is the field name or the gene */
         if (self.conf.clusterField)
@@ -566,7 +586,7 @@ function CbDbFile(url) {
                 onProgress, metaInfo);
     }
 
-    this.loadMetaVec = function(metaInfo, onDone, onProgress, otherInfo) {
+    this.loadMetaVec = function(metaInfo, onDone, onProgress, otherInfo, strategy) {
     /* get an array of numbers, one per cell, that reflect the meta field contents
      * and an object with some info about the field. call onDone(arr, metaInfo) when done.
      * Keep all compressed arrays in metaCache;
@@ -597,7 +617,13 @@ function CbDbFile(url) {
             if (metaInfo.arrType==="float32") {
                 // numeric arrays have to be binned on the client. They are always floats.
                 console.time("discretize "+metaInfo.name);
-                var discRes = discretizeArray(arr, self.exprBinCount, FLOATNAN);
+                var discRes;
+
+                if (strategy==="range")
+                    discRes = discretizeArray_binSize(arr, self.exprBinCount, FLOATNAN);
+                else
+                    discRes = discretizeArray(arr, self.exprBinCount, FLOATNAN);
+
                 console.timeEnd("discretize "+metaInfo.name);
                 metaInfo.origVals = arr; // keep original values, so we can later query for them
                 arr = discRes.dArr;
@@ -716,10 +742,12 @@ function CbDbFile(url) {
     }
 
     function discretizeArray(arr, maxBinCount, bin0Val) {
-        /* discretize numeric values to deciles. return an obj with dArr and binInfo */
-        /* bin0Val is the value that is treated differently, it is kept in its own bin */
+        /* This is the default for most users: discretize numeric values to
+         * deciles. return an obj with dArr and binInfo */
+        /* bin0Val is the value that is treated differently, it is kept in its
+         * own bin */
         /* is bin0Val is null, switch off special bin0Value handling
-        /* ported from Python cbAdd:discretizeArray */
+        /* Code ported from Python cbAdd:discretizeArray */
         /* supports NaN special values */
         var breaks = [];
 
@@ -938,9 +966,20 @@ function CbDbFile(url) {
             for (let r of loadedRanges) {
                 arrs.push(r.arr);
                 if (r.desc!=="")
-                    geneDescs.push(r.desc);
+                    geneDescs.push(r.name);
             }
-            let geneDesc = geneDescs.join("; ");
+
+            // set gene description to an ;-separated list for multi-gene mode and
+            // to chrom:minStart-maxStart for ATAC mode
+            let geneDesc;
+            if (self.isAtacMode()) {
+                let chrom = loadedRanges[0].name.split("|")[0];
+                let minStart = loadedRanges[0].name.split("|")[1];
+                let maxEnd = loadedRanges[loadedRanges.length-1].name.split("|")[2];
+                geneDesc = chrom+":"+minStart+"-"+maxEnd;
+            }
+            else
+                geneDesc = geneDescs.join("; ");
 
             // specVal is the value for a special bin, usually 0
             var specVal = 0;
@@ -1277,6 +1316,8 @@ function CbDbFile(url) {
         // first we need to lookup the offset of the line and its length from the index
         var url = cbUtil.joinPaths([self.url, "meta.index"]);
         var start = (cellIdx*6); // four bytes for the offset + 2 bytes for the line length
+        if (self.conf.metaNeedsEightBytes)
+            start = (cellIdx*10); // meta files > 4GB need 8 bytes for the offset + 2 for the line length
         var end   = start+6;
 
         function lineDone(text) {
@@ -1288,7 +1329,12 @@ function CbDbFile(url) {
 
         function offsetDone(arr) {
             /* called when the offset in meta.index has been read */
-            var offset = cbUtil.baReadOffset(arr, 0);
+            var offset;
+            if (self.conf.metaNeedsEightBytes)
+                offset = cbUtil.baReadBigOffset(arr, 0);
+            else
+                offset = cbUtil.baReadOffset(arr, 0);
+
             var lineLen = cbUtil.baReadUint16(arr, 4);
             // now get the line from the .tsv file
             var url = cbUtil.joinPaths([self.url, "meta.tsv"]);
@@ -1608,7 +1654,7 @@ function CbDbFile(url) {
                   //alert("Error: "+sym+" is in quick genes list but is not a valid gene");
                   //continue;
                //}
-               if (geneId.indexOf("|")!==-1)
+               if (geneId.indexOf("|")!==-1 && !self.conf.atacSearch)
                    geneId = geneId.split("|")[0];
 
                 self.loadExprAndDiscretize(