Merge branch 'develop'

cellbrowserData/genes/log.txt

@@ -6,3 +6,4 @@ wget ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.
 wget ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz -O - | zcat | cut -f2,3 | grep -v ^Gene > entrez-mouse.symbols.tsv
 zcat entrez-human.symbols.tsv.gz | cat - entrez-mouse.symbols.tsv > entrez.symbols.tsv
 cp entrez.symbols.tsv.gz ~/htdocs-cells/downloads/cellbrowserData/genes/
+cp /hive/data/outside/gencode/tsv/gencode28.genes.bed ./hg38.gencode28.genes.bed

cellbrowserData/genomes/barChartBed.as

@@ -7,7 +7,7 @@ table barChartBed
     string name;        "Gene identifier"
     uint   score;       "Score from 0-1000, typically derived from total of median value from all categories"
     char[1] strand;     "+ or - for strand. Use . if not applicable"
-    string name2;       "Gene name"
+    string name2;       "Gene symbol"
     uint expCount;      "Number of categories"
     float[expCount] expScores; "Comma separated list of category values"
     bigint _dataOffset; "Offset of sample data in data matrix file, for boxplot on details page"

docs/seurat.rst

@@ -9,8 +9,8 @@ There are a number of ways to create a cell browser using Seurat:
 
 Each of these methods are described in more detail below.
 
-Convert a Seurat ``rds`` file
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Convert a Seurat ``rds`` or ``.rdata` file
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 First, create an .rds file in R as described in the Seurat tutorial::
 
@@ -21,8 +21,9 @@ file into a cell browser::
 
     cbImportSeurat -i pbmc3k_small.rds -o pbmc3kImport
 
-This works with objects created by versions 2 and 3 of Seurat. Make sure that
-you have the same major version of Seurat installed that was used to create the
+This works with objects created by versions 2 and 3 of Seurat. ``cbImportSeurat`` can read 
+both ``.rds`` and ``.rdata`` files, for `.rdata` it assume the first object is the Seurat object.
+Make sure that you have the same major version of Seurat installed that was used to create the
 object. You cannot open Seurat2 objects with Seurat3 or vice versa. 
 (We often need to switch between Seurat versions and found conda environments very helpful for this.)
 

src/cbPyLib/cellbrowser/R/ExportToCellbrowser-seurat.R

@@ -66,8 +66,9 @@ findMatrix = function( object, matrix.slot ) {
 #' exprMatrix.tsv, tsne.coords.tsv, meta.tsv, markers.tsv and a default cellbrowser.conf
 #' @param dataset.name name of the dataset. Defaults to Seurat project name
 #' @param reductions vector of reduction names to export, defaults to all reductions.
-#' @param markers.file path to file with marker genes. Alternatively,
-#' markers can also be supplied in the object, as misc$markers.
+#' @param markers.file path to file with marker genes. By defaults, marker
+#' are searched in the object itself as misc$markers. If none are supplied in 
+#' object or via this argument, they are recalculated with \code{FindAllMarkers}
 #' @param markers.n if no markers were supplied, FindAllMarkers is run.
 #' This parameter indicates how many markers to calculate, default is 100
 #' @param matrix.slot matrix to use, default is 'counts'
@@ -86,7 +87,7 @@ findMatrix = function( object, matrix.slot ) {
 #' @param skip.metadata whether to skip exporting metadata
 #' @param skip.reductions whether to skip exporting reductions
 #' @param port on which port to run UCSC cellbrowser webserver after export
-#' @param ... specifies the metadata fields to export. To supply field with
+#' @param ... specifies the metadata fields to export. To supply a field name and its
 #' human readable name, pass name as \code{field="name"} parameter.
 #'
 #' @return This function exports Seurat object as a set of tsv files
@@ -101,9 +102,10 @@ findMatrix = function( object, matrix.slot ) {
 #'
 #' @author Maximilian Haeussler, Nikolay Markov
 #'
+#' @importFrom tools file_ext
 #' @importFrom utils browseURL
 #' @importFrom reticulate py_module_available import
-#' @importFrom tools file_ext
+#' @importFrom Seurat Project Idents GetAssayData Embeddings FetchData
 #'
 #' @export
 #'

src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js

@@ -949,9 +949,8 @@ var cellbrowser = function() {
 
     function openDatasetDialog(openDsInfo, selName) {
     /* build dataset open dialog, 
-     * - datasetList is the list of all datasets to show on the left, null to hide list
      * - openDsInfo is the currently open object or a collection. 
-     * - openCollection is true to show 'collection' decorations: summary entry, note at the top and back link
+     * - selName is the currently selected dataset in this list
      */
 
         var datasetList = [];
@@ -1142,8 +1141,11 @@ var cellbrowser = function() {
 
         var buttons = [];
         if (db!==null) {
+            var cancelLabel = "Cancel";
+            if (onlyInfo)
+                cancelLabel = "Close";
             buttons.push( {
-                text:"Cancel", 
+                text: cancelLabel, 
                 click: function() { 
                     $( this ).dialog( "close" ); 
                     if (openDsInfo.isCollection)
@@ -1566,7 +1568,8 @@ var cellbrowser = function() {
         }
     }
 
-    function addNewAnnotation(fieldLabel, newMetaValue, cellIds) {              var metaInfo;
+    function addNewAnnotation(fieldLabel, newMetaValue, cellIds) {              
+        var metaInfo;
         let cellCount = db.conf.sampleCount;
         if (!db.getMetaFields()[0].isCustom) {
             // add a new enum meta field
@@ -2372,8 +2375,6 @@ var cellbrowser = function() {
        $('#tpTutorialButton').click( function()  { showIntro(false); } );
        $('#tpAboutButton').click( onAboutClick );
        $('#tpOpenDatasetLink').click( openCurrentDataset );
-       //$('#tpOpenDatasetLink').click( function() { 
-           //openDatasetDialog(db.conf, db.name); } );
        $('#tpSaveImage').click( onSaveAsClick );
        $('#tpSelectAll').click( onSelectAllClick );
        $('#tpSelectNone').click( onSelectNoneClick );
@@ -4007,12 +4008,14 @@ var cellbrowser = function() {
             metaCounts[valIdx].push(valIdx);
 
         var oldSortBy = getFromUrl("SORT");
+        // URL overrides default value
         if (sortBy===undefined && oldSortBy!==undefined)
             sortBy = oldSortBy;
-        if (sortBy===undefined && db.conf.sortBy)
-            sortBy = db.conf.sortBy[metaInfo.label];
-
-        if (sortBy!==undefined && sortBy!=="freq" && sortBy!=="name") {
+
+        // default sorting can be specfied with "sortBy" in cellbrowser.conf
+        if (sortBy===undefined && metaInfo.sortBy)
+            sortBy = metaInfo.sortBy;
+        if (sortBy!==undefined && sortBy!=="freq" && sortBy!=="name" && sortBy!=="none") {
             alert("sortBy is '"+cleanString(sortBy)+' but it can only be "freq" or "name"');
             sortBy = undefined;
         }
@@ -4040,14 +4043,11 @@ var cellbrowser = function() {
         //var defaultColors = makeColorPalette(countListSorted.length, useGradient);
 
         var rows = [];
-        //var defColIdx = 0;
         var shortLabels = metaInfo.ui.shortLabels;
         var longLabels = metaInfo.ui.longLabels;
         for (var legRowIdx = 0; legRowIdx < countListSorted.length; legRowIdx++) {
             var legRowInfo = countListSorted[legRowIdx];
-            //var label = legRowInfo[0];
             let valIdx = legRowInfo[2]; // index of the original field in fieldInfo
-            //let valIdx = legRowInfo.intKey;
             var label = shortLabels[valIdx];
 
             var desc  = null;
@@ -4345,7 +4345,12 @@ var cellbrowser = function() {
             resizeDivs(true);
 
             if (!db.conf.metaFields) {
-                showCollectionDialog(datasetName);
+                // pablo often has single-dataset installations, there is no need to open the
+                // dataset selection box then.
+                if (db.conf.datasets.length===1 && datasetName==="") // "" is the root dataset
+                    loadDataset(db.conf.datasets[0].name, false);
+                else
+                    showCollectionDialog(datasetName);
                 return;
             }
 
@@ -4358,6 +4363,9 @@ var cellbrowser = function() {
 
             cartLoad(db);
             renderData();
+
+            if (getVar("openDialog"))
+                openDatasetDialog(db.conf, db.name); // open Info dialog
             cartSave(db); // = set the current URL from local storage settings
 
             // start the tutorial after a while
@@ -5202,36 +5210,18 @@ var cellbrowser = function() {
 
     function sortPairsBy(countList, sortBy) {
     /* sort an array in the format [name, count] by either name (using naturalSort) or count */
-    // XX no need anymore to return a dict, just return the list
-        // convert the dict to a list of (count, key)
-        //var countList = [];
-        //var numCount = 0;
-        //var count = null;
-        //var useGradient = false; // use a rainbow or gradient palette?
-        //for (var key in dict) {
-            //count = dict[key];
-            //if (!isNaN(key)) // key looks like a number
-                //numCount++;
-            //countList.push( [count, key] );
-        //}
-
-        // auto-detect: sort list by name if most names are numbers
-        //if ((countList.length >= 4 && numCount >= countList.length-1)) {
-            //if (sortBy===undefined)
-                //sortBy = "name";
-            //useGradient = true;
-        //}
-
         var isSortedByName = null;
 
         if (sortBy==="name") {
             countList.sort(function(a, b) { return naturalSort(a[0], b[0]); });  // I have a feeling that this is very slow...
             isSortedByName = true;
         }
-        else {
+        else if (sortBy=="count") {
             // sort this list by count
             countList = countList.sort(function(a, b){ return b[1] - a[1]; }); // reverse-sort by count
             isSortedByName = false;
+        } else {
+            isSortedByName = false;
         }
 
         var ret = {};