cellbrowser 1.2.8__tar.gz → 1.2.11__tar.gz

cellbrowser-1.2.11/PKG-INFO

@@ -0,0 +1,37 @@
+Metadata-Version: 2.2
+Name: cellbrowser
+Version: 1.2.11
+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
+Author-email: max@soe.ucsc.edu
+License: GPL 3
+Classifier: Programming Language :: Python :: 2
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: JavaScript
+Requires-Python: >=2.5
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-python
+Dynamic: summary
+
+The UCSC Cell Browser is an interactive browser for
+    single cell data, like mRNA or ATAC-seq data. You can display
+    dimensionality reductions, navigate them with the mouse or the cursor keys,
+    select cells, color by genes or meta annotations and make many other
+    changes. The main site runs at https://cells.ucsc.edu, but using this
+    package you can also convert data yourself and build a Cell Browser HTML
+    directory that can be served through any University or any other webserver
+    for static webpages. You can try the Cell Browser at https://cells.ucsc.edu
+    or read about how to convert data with this package on
+    https://cellbrowser.rtfd.org.
+
+    We strongly recommend that to use Python3, but we make an effort to remain compatible with Python2.

{cellbrowser-1.2.8 → cellbrowser-1.2.11}/setup.cfg

@@ -1,9 +1,10 @@
 [versioneer]
-vcs = git
+VCS = git
 style = pep440-pre
 versionfile_source = src/cbPyLib/cellbrowser/_version.py
 versionfile_build = cellbrowser/_version.py
-tag_prefix = 
+tag_prefix = v
+parentdir_prefix = cellbrowser-
 
 [build_ext]
 inplace = 1

{cellbrowser-1.2.8 → cellbrowser-1.2.11}/src/cbPyLib/cellbrowser/R/cellbrowser.R

@@ -381,21 +381,20 @@ ExportToCellbrowser <- function(
   }
   if (is.null(markers.file) && !skip.markers) {
     if (length(levels(Idents(object))) > 1) {
-      markers.helper <- function(x) {
-        partition <- markers[x,]
+      #markers.helper <- function(x) {
+        #partition <- markers[x,]
 
         # Seurat4 changed the field name! grrrr...
-        if ("avg_log2FC" %in% colnames(markers))
-            avgs <- -partition$avg_log2FC
-        else
-            avgs <- -partition$avg_logFC
-
-        ord <- order(partition$p_val_adj < 0.05, avgs)
-        res <- x[ord]
-        naCount <- max(0, length(x) - markers.n)
-        res <- c(res[1:markers.n], rep(NA, naCount))
-        return(res)
-      }
+        #if ("avg_log2FC" %in% colnames(markers))
+            #avgs <- -partition$avg_log2FC
+        #else
+            #avgs <- -partition$avg_logFC
+        #ord <- order(partition$p_val_adj < 0.05, avgs)
+        #res <- x[ord]
+        #naCount <- max(0, length(x) - markers.n)
+        #res <- c(res[1:markers.n], rep(NA, naCount))
+        #return(res)
+      #}
       if (.hasSlot(object, "misc") && !is.null(x = object@misc["markers"][[1]])) {
         message("Found precomputed markers in obj@misc['markers']")
         markers <- object@misc["markers"]$markers
@@ -404,15 +403,18 @@ ExportToCellbrowser <- function(
         markers <- FindAllMarkers(
           object,
           do.print = TRUE,
-          print.bar = TRUE,
-          test.use = "wilcox",
-          logfc.threshold = 0.25
+          only.pos = TRUE,
+          logfc.threshold = 0.25,
+          min.pct = 0.25
         )
       }
       message("Writing top ", markers.n, ", cluster markers to ", fname)
-      markers.order <- ave(x = rownames(x = markers), markers$cluster, FUN = markers.helper)
-      top.markers <- markers[markers.order[!is.na(x = markers.order)], ]
-      write.table(x = top.markers, file = fname, quote = FALSE, sep = "\t", col.names = NA)
+      #markers.order <- ave(x = rownames(x = markers), markers$cluster, FUN = markers.helper)
+      #top.markers <- markers[markers.order[!is.na(x = markers.order)], ]
+      require(dplyr);
+      #markers  %>% group_by(cluster) %>% top_n(n = markers.n, wt = avg_logFC)
+      markers %>% group_by(cluster) %>% dplyr::filter(avg_log2FC > 1) %>% slice_head(n = markers.n) %>% ungroup() -> topMarkers
+      write.table(x = topMarkers, file = fname, quote = FALSE, sep = "\t", col.names = NA)
     } else {
       message("No clusters found in Seurat object and no external marker file provided, so no marker genes can be computed")
       file <- NULL

cellbrowser-1.2.11/src/cbPyLib/cellbrowser/__init__.py

@@ -0,0 +1,4 @@
+# empty init, nothing to do here
+
+from . import _version
+__version__ = _version.get_versions()['version']

{cellbrowser-1.2.8 → cellbrowser-1.2.11}/src/cbPyLib/cellbrowser/_version.py

@@ -1,5 +1,5 @@
 
-# This file was generated by 'versioneer.py' (0.18) from
+# This file was generated by 'versioneer.py' (0.29) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-07-09T12:41:36-0700",
+ "date": "2025-01-31T10:12:36-0800",
  "dirty": false,
  "error": null,
- "full-revisionid": "0775adae1db21db211175fe6099fd4217f7a21ac",
- "version": "v1.2.8"
+ "full-revisionid": "bc2a38bfa21dd92e505693b264f0cef876890b17",
+ "version": "1.2.11"
 }
 '''  # END VERSION_JSON
 

{cellbrowser-1.2.8 → cellbrowser-1.2.11}/src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css

@@ -48,6 +48,10 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
         margin-right: 6px;
 }
 
+.tpTitle {
+        z-index: 100;
+}
+
 .tpGeneExprCombo {
         margin-left: 6px;
         margin-right: 6px;
@@ -92,6 +96,7 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
         position : absolute;
         display: grid;
         grid-template-columns: 45px 120px 15px;
+        background: rgba(255,255,255,0.5);
 }
 
 .sliderLabel {
@@ -130,8 +135,9 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 .ui-menu-item { font-size:13px }
 .ui-menu .ui-menu-item-wrapper { padding: 1px 1em 1px .4em; }
 .ui-tooltip { font-size: 13px }
-#tpButtonInfo { height: 24px; top: 1px; margin-right: 8px; width: 120px; border-radius: 4px }
+#tpButtonInfo { height: 24px; top: 1px; margin-right: 8px; border-radius: 4px; padding-top: 4px }
 .tpDialogInput { margin-left: 12px; margin-top: 5px; margin-bottom: 12px; }
+#tpDialog { z-index: 1001; }}
 
 .tpIconButton { 
         padding: 1px 2px 1px 2px; 
@@ -168,6 +174,13 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
         cursor: pointer; 
 }
 
+.tpSameLink {
+    text-decoration: underline; 
+    cursor: pointer; 
+    color: darkgrey; 
+    float: right
+}
+
 .tpDatasetPane {
         padding-top: 10px !important;
         border-radius: 4px;
@@ -319,12 +332,15 @@ input[type=checkbox], input[type=radio] {
 }
 
 .tpMetaBox { font-size: 13px; cursor:default; overflow:hidden }
-.tpMetaHover { color: #FFF; background-color: #666}
+.tpMetaHover { 
+        color: white; 
+        background-color: #333 !important;
+}
 .tpMetaLabel { font-weight: bold; padding-left: 2px}
 .tpMetaLabelGrey { color: #666666}
 .tpMetaMultiVal { font-style: italic; color: gray }
 .tpMetaHistLabel { text-decoration: underline; color: blue }
-.tpMetaValue { height: 1.3em; margin-left: 8px; padding-left: 3px; background-color:#EEE; }
+.tpMetaValue { height: 1.3em; padding-left: 3px; background-color:#EEE; }
 .tpMetaSelect { outline: 2px solid black; background-color: #DEDEDE }
 .tpMetaValueSelect { background-color: #CCC}
 .tpMetaPerc { color:grey; float:right }
@@ -342,7 +358,7 @@ button { line-height: 12px }
 .btn-default { background: linear-gradient(#fff 20%, #f7f7f7 60%, #f5f5f5 100%) }
 
 #tpButtonBar {display: block; }
-.tpButton { border-radius: 0; font-size: 15px; display: inline-block; background-color: #f6f6f6; border: 1px solid #c5c5c5; margin: 1px 3px 1px 1px; padding: 1px 3px 1px 3px; cursor:default; vertical-align: middle; user-select: none}
+.tpButton { border-radius: 0; font-size: 15px; display: inline-block; background-color: #f6f6f6; border: 1px solid #c5c5c5; margin: 1px 3px 1px 1px; padding: 1px 3px 1px 3px; cursor:default; vertical-align: middle; user-select: none; }
 .tpButton:active { background-color: #888; }
 .tpButton active { background-color: #888; }
 .tpButton:hover { background-color: #eee }

{cellbrowser-1.2.8 → cellbrowser-1.2.11}/src/cbPyLib/cellbrowser/cbWeb/js/cbData.js

@@ -480,6 +480,15 @@ function CbDbFile(url) {
         }
     }
 
+    this.findCoordIdx = function(name) {
+        /* given coord label return its index */
+        coords = self.conf.coords;
+        for (let i=0; i<coords.length; i++) {
+            if (coords[i].name===coordLabel)
+                return i;
+        }
+    }
+
     this.loadCoords = function(coordIdx, onDone, onSpatialDone, onProgress) {
     /* load coordinates from URL and call onDone(array of (x,y), coordInfoObj, labelMids) when done */
         var i = 0;
@@ -487,6 +496,17 @@ function CbDbFile(url) {
         var meta = null;
         var labelMids; // null means: no json file found
 
+        var coordInfo = self.conf.coords[coordIdx];
+        if (coordInfo===null) {
+           alert("Could not find coordinates with name "+this.coordName);
+           return;
+        }
+
+        let hasSpatial = coordInfo.images || self.conf.spatial;
+
+        //if (hasSpatial && coordInfo.aspectRatio===undefined)  // patch up old datasets
+            //coordInfo.aspectRatio = 1.0
+
         function binDone(data, other) {
             binData = data;
             meta = other;
@@ -505,13 +525,7 @@ function CbDbFile(url) {
             return;
         }
 
-        var coordInfo = self.conf.coords[coordIdx];
-        if (coordInfo===null) {
-           alert("Could not find coordinates with name "+this.coordName);
-           return;
-        }
-
-        if (coordInfo.images || self.conf.spatial) {
+        if (hasSpatial) {
            var spatials = coordInfo.images;
                if (!spatials)// older placement of the object
                    spatials = self.conf.spatial; //now spatial settings must be on the coords to support multi-coord datasets
@@ -547,7 +561,7 @@ function CbDbFile(url) {
     };
 
     this.getDefaultColorField = function() {
-        /* return a pair: [0] is "meta" or "gene" and [1] is the field name or the gene */
+        /* return the meta field to colors on */
         if (self.conf.clusterField)
             return self.conf.clusterField; // just for backwards-compat. with old datasets
         else
@@ -853,15 +867,22 @@ function CbDbFile(url) {
 
     this.locusToOffset = function(name) {
         /* for both gene and ATAC mode: */
-        /* return an array [start, end, name] given a locus description (=a string: gene symbol or chr|start|end) */
+        /* return an array [start, end, name] given a locus description (=a string: gene ID/symbol or chr|start|end) */
         var off = null;
+        var geneId = name;
         //if (name.includes("|")) { // atac mode: name is chrom|start|end
         if (self.peakOffsets !== null) { // atac mode: name is chrom|start|end
             let pos = name.split("|");
             off = self.findAtacOffsets(pos[0], parseInt(pos[1]), parseInt(pos[2]));
         }
         else {
-            off = self.geneOffsets[name];
+            var geneIds = self.findGenesExact(name);
+            if (geneIds.length!==0) {
+                geneId = geneIds[0];
+                off = self.geneOffsets[geneIds[0]];
+                if (geneIds.length>1)
+                    alert("More than one match for gene name "+name+", using only first match.");
+            }
         }
 
         if (off===null || off===undefined) {
@@ -872,7 +893,7 @@ function CbDbFile(url) {
         let start = off[0];
         let len = off[1];
         let end = start+len;
-        return [start, end, name];
+        return [start, end, geneId];
     }
 
     this.namesToChunks = function(lociNames) {
@@ -1382,19 +1403,22 @@ function CbDbFile(url) {
 	return lo;
     }
 
-    function updateGeneSyns(geneSyns, name) {
+    function addToGeneSynsAndSplit(geneSyns, name) {
         /* given a symbol which can be geneId|sym, append to geneSyn array 1 or 2 tuples with [searchKey, geneId] */
+        var geneId = name;
+        var sym = name;
         if (name.indexOf("|")===-1) {
             // datasets with only one gene name: old behavior
             geneSyns.push( [name.toLowerCase(), name] );
         } else {
             // dataset with geneId and symbol
             var parts = name.split("|");
-            var geneId = parts[0];
-            var sym = parts[1];
+            geneId = parts[0];
+            sym = parts[1];
             geneSyns.push( [geneId.toLowerCase(), geneId] );
             geneSyns.push( [sym.toLowerCase(), geneId] );
         }
+        return [geneId, sym];
     }
 
     this.indexGenes = function() {
@@ -1405,24 +1429,16 @@ function CbDbFile(url) {
         var newIdx = {};
         var geneIdx = self.geneOffsets;
         var geneSyns = [];
-        for (var key in geneIdx) { // as of 2019, faster than Object.entries()
-            updateGeneSyns(geneSyns, key);
-
-            var val = geneIdx[key];
-            var sym = key;
-            var geneId = key;
-            if (key.indexOf("|")!==-1) {
-                var parts = key.split("|");
-                geneId = parts[0];
-                sym = parts[1];
-            }
-
-            var newVal = [val[0], val[1], sym];
-            newIdx[geneId] = newVal;
-                
-            self.geneOffsets=newIdx;
-            self.geneSyns = geneSyns;
-        }
+        for (var geneName in geneIdx) { // as of 2019, faster than Object.entries()
+            // a geneName can be either a single symbol or a string like geneId|sym
+            var offsets = geneIdx[geneName];
+            var geneIdSym = addToGeneSynsAndSplit(geneSyns, geneName);
+            var geneId = geneIdSym[0];
+            var sym = geneIdSym[1];
+            newIdx[geneId] = [offsets[0], offsets[1], sym];
+        }
+        self.geneOffsets=newIdx;
+        self.geneSyns = geneSyns;
     }
 
     function searchGeneNames(geneSyns, searchStr) {
@@ -1437,7 +1453,7 @@ function CbDbFile(url) {
         return foundIds;
     }
 
-    this.findGeneIds = function(searchStr) {
+    this.findGeneIdsPrefixSuffix = function(searchStr) {
         /* return an array of matching geneIds for searchStr, uses self.geneSyns */
         searchStr = searchStr.toLowerCase();
         var geneSyns = self.geneSyns;
@@ -1452,7 +1468,7 @@ function CbDbFile(url) {
      * returns an array of objects with .id and .sym.
      * There is a version using this for ATAC mode, see findGenesAtac()
      * */
-        var foundIds = self.findGeneIds(searchStr);
+        var foundIds = self.findGeneIdsPrefixSuffix(searchStr);
         var geneNameObjs = [];
         for (var geneId of foundIds)
             geneNameObjs.push(self.getGeneInfo(geneId)); // for selectizeSendGenes
@@ -1460,10 +1476,10 @@ function CbDbFile(url) {
         return geneNameObjs;
     };
 
-    this.findGenesExact = function(geneSyns, geneSym) {
+    this.findGenesExact = function(geneSym) {
         /* search the geneSyns (arr of [syn, geneId]) for matches. Return arr of geneIds 
          * Used to resolve symbol to geneId (symToGene)*/
-        geneSym = geneSyns.toLowerCase();
+        geneSym = geneSym.toLowerCase();
         var geneSyns = self.geneSyns;
         var foundIds = [];
         for (var i=0; i<geneSyns.length; i++) {
@@ -1475,6 +1491,27 @@ function CbDbFile(url) {
         return foundIds;
     }
 
+    this.mustFindOneGeneExact= function(symOrId) { 
+        /* given a geneId or symbol, return the geneId. If 0 or >1 are found, abort and show error message. */
+        if (symOrId.indexOf("|")!==-1)
+            symOrId = symOrId.split("|")[0];
+
+        let geneIds = self.findGenesExact(symOrId);
+        if (geneIds.length===0) {
+            alert("Could not find gene symbold or ID: "+symOrId);
+            return null;
+        }
+        if (geneIds.length>1) {
+            alert("Found more than one geneId for symbol, using only the first match: "+symOrId);
+        }
+        return geneIds[0];
+    }
+
+    this.isGeneId = function (geneId) {
+        /* check if a given string is a geneId */
+        return (geneId in self.geneOffsets);
+    }
+
     function pickTssForGene(loc) {
         /* given a chromLoc tuple (start, end, strand, sym), return the TSS of the gene (start or end )*/
         var start = loc[0];
@@ -1530,7 +1567,7 @@ function CbDbFile(url) {
     this.findGenesAtac = function(searchStr) {
         /* like findGenes(), but for ATAC mode: return an array of {.id and .sym} given a search string  */
         //var geneInfos = cbUtil.searchKeys(self.geneToTss, searchStr);
-        var geneIds = self.findGeneIds(searchStr);
+        var geneIds = self.findGeneIdsPrefixSuffix(searchStr);
 
         if (geneIds.length===0)
             return [];
@@ -1666,7 +1703,7 @@ function CbDbFile(url) {
                    },
                    onProgress, strategy);
            }
-       }
+        }
     };
 
     this.loadGeneSetExpr = function(onDone) {