cellbrowser 1.2.15.post0.dev8__tar.gz → 1.2.17__tar.gz

{cellbrowser-1.2.15.post0.dev8/src/cbPyLib/cellbrowser.egg-info → cellbrowser-1.2.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.15.post0.dev8
+Version: 1.2.17
 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-1.2.15.post0.dev8 → cellbrowser-1.2.17}/README.rst

@@ -12,21 +12,38 @@ spatial gene/ATAC, multi-modal combinations of these and trajectory lines.
 It comes with one-line data exporters for all common analysis formats: Seurat, Scanpy, Cellranger, Monocle and 
 you can always use tsv/csv files to import your data. The exporters are part of Seurat 3/4 and Scanpy. 
 
-To look at a list of selected single cell datasets, see http://cells.ucsc.edu
-
-To setup your own cell browser, from Cellranger, Seurat, Scanpy or text files 
+Here are a few datasets that demonstrate these features:
+
+- A simple gene expression dataset: https://cortex-dev.cells.ucsc.edu
+- ATAC support https://cortex-atac.cells.ucsc.edu
+- Spatial transcriptomics support https://ms-subcortical-lesions.cells.ucsc.edu
+- Split screen mode to display both the spatial and snRNA-seq data side by side https://cells.ucsc.edu/?ds=dup15q-cortex-organoids+spatial+control
+- Pseudotime cell trajectories from Monocle3 https://cells-test.gi.ucsc.edu/?ds=pre-postnatal-cortex+ex-neu+rna
+- Tree-like cell trajectories from URD https://cells.ucsc.edu/?ds=cardiac-differentiation+trajectory+cm-combined-trajectory
+- Clone lineage tracing support: color by the field CellTag, select tags in the legend, then click "recolor checked": https://cells.ucsc.edu/?ds=gbm-nvp+nvp-celltag
+- Brain lipidomics https://cells.ucsc.edu/?ds=brain-lipids
+
+To show all our > 300 single cell datasets, see http://cells.ucsc.edu
+
+To upload datasets for the cells.ucsc.edu website, use https://cells-submit.gi.ucsc.edu. Or email us at cells@ucsc.edu. We reply usually on the same day.
+
+Most users prefer uploading their datasets to us rather than hosting them on their own webserver.
+Our webserver is reliable, fast and we take care
+of adding new features and keeping the data online. 
+But, if you really want to make your own website, to setup your own cell
+browser, on your own web server, from Cellranger, Seurat, Scanpy or text files
 (tsv/csv), or just a single cell expression matrix, read the documentation
-at http://cellbrowser.rtfd.io. If you use the UCSC Cell Browser in your research, please cite
+at http://cellbrowser.rtfd.io.
+
+If you use the UCSC Cell Browser in your research, please cite
 `our Bioinformatics paper <https://dx.doi.org/10.1093/bioinformatics/btab503>`_.
 If you are also using data from a specific dataset we host, please also cite
 the original authors of that dataset (visible under 'Info & Download' while viewing that dataset).
 
-If you want us to add a single cell dataset to the website http://cells.ucsc.edu, 
-please contact us at cells@ucsc.edu. We are happy to add any dataset.
-
 This is a viewer for a static, precomputed layout. If you're looking for an interative layout, where you can 
 move the cells around and run some algorithms interactively, try Chan-Zuckerberg's own cellxgene or Spring.
-A website with both datasets and some analysis is `Scope <http://scope.aertslab.org/>`_.
+Another website with both datasets and some analysis is `Scope <http://scope.aertslab.org/>`_. There are many other
+similar websites now, usually with a few dozen datasets.
 
 Many labs host their data at cells.ucsc.edu by sending it to us, but some groups have setup their own cell browsers:
 
@@ -48,8 +65,7 @@ Many labs host their data at cells.ucsc.edu by sending it to us, but some groups
 * 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:
+These are some papers that reference cell browsers made at UCSC but there are many more, search for "cells.ucsc.edu" in Google Scholar to find more:
 
 * organoidatlas: https://www.sciencedirect.com/science/article/pii/S221112472030053X
 * dros-brain: https://elifesciences.org/articles/50354
@@ -59,8 +75,9 @@ These papers have cell browsers made at UCSC:
 
 Before judging this project by the number of issue tickets or PRs, note that at UCSC we use an internal
 ticket system with more features and that a lot of communication with wetlab users is by email at cells@ucsc.edu, as we 
-do not require a Github account for feedback. But we do reply to issues here, as you can see from the Github 
-account and also use Github for source control.
+do not require a Github account for feedback, as our submitters are biologists, not computer scientists.
+But we do reply to issues here, as you can see from the Github account and also use Github for source control, and 
+we get emails every day. The project is much more active than the Github issues suggest.
 
 Install and use
 ---------------
@@ -72,9 +89,9 @@ Install and use
 * Galaxy: there is a Galaxy tool for UCSC CellBrowser, which can be installed on any Galaxy instance via its `Galaxy Toolshed entry <https://toolshed.g2.bx.psu.edu/view/ebi-gxa/ucsc_cell_browser>`_ or it can be directly used by users at the `Human Cell Atlas Galaxy instance <https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/ucsc_cell_browser/ucsc_cell_browser>`_ or as part of the example workflows, such as the `Human Cell Atlas / Scanpy CellBrowser workflow <https://humancellatlas.usegalaxy.eu/u/pmoreno/w/humancellatlas-scanpy-cellbrowser>`_ or the `EBI Single Cell Expression Atlas / Scanpy / CellBrowser workflow <https://humancellatlas.usegalaxy.eu/u/pmoreno/w/atlas-scanpy-cellbrowser-imported-from-uploaded-file>`_
 
 This project was funded by the California Institute of Regenerative Medicine and the
-Chan-Zuckerberg Initiative https://www.chanzuckerberg.com/. In 2020, it was funded through a supplement to the NHGRI Genome Browser grant. Since 2023, it is funded by a grant from NIMH BRAIN.
+Chan-Zuckerberg Initiative https://www.chanzuckerberg.com/. In 2020, it was funded through a supplement to the NHGRI Genome Browser grant. Since 2023, it is funded by a grant from NIMH BRAIN and a DISC0 from CIRM.
 
-This is early research software. You are likely to find bugs. Please open a Github
+This is early research software. It may contain bugs. Please open a Github
 ticket or email us at cells@ucsc.edu, we can usually fix them quickly.
 
 Citation

{cellbrowser-1.2.15.post0.dev8 → cellbrowser-1.2.17}/src/cbPyLib/cellbrowser/R/cellbrowser.R

@@ -87,6 +87,28 @@ exportImages <- function(obj, outDir, embeddings.conf) {
     require(png)
     for (name in names(obj@images)) { 
         message(name); 
+        # SlideSeq-class SpatialImage objects do not contain a bitmap image
+        # They only contain a coordinates df, so test if this image is a SlideSeq
+        # And process using this code block (instead of usual steps further below)
+        if ("SlideSeq" %in% class(obj@images$image)[1]) {
+            coordsPath <- file.path(outDir, paste0(name, ".coords.tsv"))
+            message("Writing coords for image to ", coordsPath)
+            coords <- GetTissueCoordinates(object = obj[[name]])
+            # One of the columns I want to delete is currently named 'NA' for
+            # a missing value
+            colnames(coords)[3] <- "missing"
+            # Delete columns 3 and 4 by name, keeping columns 1 and 2 for printing out
+            coords = subset(coords, select = -c(missing, cells))
+
+            write.table(coords, coordsPath, sep="\t", row.names=T, quote=F, col.names=NA)
+            conf <- sprintf(
+             '  {\n    "file": "%s",\n    "shortLabel": "Spatial %s",\n   }',
+             coordsPath,
+             name
+            )
+            embeddings.conf <- c(conf, embeddings.conf)
+            return(embeddings.conf)
+        }
         img = GetImage(obj, mode="raw", image=name); 
         if (is.null(img)) {
             message("The image is not a bitmap image, cannot export yet.")
@@ -100,11 +122,18 @@ exportImages <- function(obj, outDir, embeddings.conf) {
         xMax = dim(img)[2]; # there is a difference of 3 pixels on height when comparing "identify file.jpeg" with this. NO IDEA WHY!
         coordsPath <- file.path(outDir, paste0(name, ".coords.tsv")) 
         message("Writing coords for image to ", coordsPath)
-        #coords <- GetTissueCoordinates(object = obj[[img]])
-
         coords <- GetTissueCoordinates(object = obj[[name]])
-        coordsRev <- coords[, c("imagecol", "imagerow")]  # Grrrr... Seurat stores coordinates as (y,x) in this particular case. reverse the order now.
-        colnames(coordsRev) <- c("x", "y")
+
+        if (all(c("imagecol", "imagerow") %in% colnames(coords))) {
+        # Seurat-style naming: reverse order
+          coordsRev <- coords[, c("imagecol", "imagerow")]
+          colnames(coordsRev) <- c("x", "y")
+        } else if (all(c("x", "y") %in% colnames(coords))) {
+          # Already in standard x/y format
+          coordsRev <- coords[, c("y", "x")]
+        } else {
+          stop("Error: coordinates must have either (imagecol, imagerow) or (x, y) columns.")
+        }
 
         write.table(coordsRev, coordsPath, sep="\t", row.names=T, quote=F, col.names=NA)
         conf <- sprintf(
@@ -415,9 +444,12 @@ ExportToCellbrowser <- function(
             markers <- object@misc["markers"]$markers
       } else {
         message("Running FindAllMarkers(), using wilcox test, min logfc diff 0.25")
-        if ("SCT" %in% names(object@assays)) {
+        # Only run this block if the Active assay is SCT
+        if ("SCT" %in% DefaultAssay(object = object)) {
             message("Looks like an SCT object, so running PrepSCTFindMarkers()")
-            PrepSCTFindMarkers(object = object)
+            # The results from this command need to be written back to the object prior to
+            # running FindAllMarkers
+            object <- PrepSCTFindMarkers(object = object)
         }
         markers <- FindAllMarkers(
           object,

{cellbrowser-1.2.15.post0.dev8 → cellbrowser-1.2.17}/src/cbPyLib/cellbrowser/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-05-22T14:10:47-0700",
+ "date": "2026-04-22T13:09:32-0700",
  "dirty": false,
  "error": null,
- "full-revisionid": "ebe2e27cb09c7f85bdbfee91093a58c64c8ed1b9",
- "version": "1.2.15.post0.dev8"
+ "full-revisionid": "73100b2c3973b545756150bc92f27113edf0f592",
+ "version": "1.2.17"
 }
 '''  # END VERSION_JSON
 

{cellbrowser-1.2.15.post0.dev8 → cellbrowser-1.2.17}/src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css

@@ -69,16 +69,6 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
         height:100%;
 }
 
-#tpLegendColorChecked,
-#tpLegendAll,
-#tpLegendNone,
-#tpLegendInvert,
-#tpLegendNotNull {
-  font-size: 13px;
-  margin-right: 2px;
-  margin-bottom: 2px;
-}
-
 .tpDatasetPane { 
         padding: 5px !important; 
         padding-left: 10px !important; 
@@ -117,12 +107,12 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 
 .tpLegend { font-size:13px; /* border: 2px solid transparent; */ cursor:default; word-wrap: break-word; clear:both}
 .tpLegendHl { background-color: #ccc; color: black; }
-.tpHint { font-weight:normal; line-height:1.4; font-size: 80%}
-#tpLegendHeader { background-color:#eee; color: #777 }
+.tpHint { font-weight:normal; line-height:1.4; font-size: 80%; margin-top:4px}
+#tpLegendHeader { background-color:#eee; color: #777; margin-top: 2px}
 #tpLegendTitle { font-weight: bold }
 #tpLegendSubTitle { font-size: 80%; font-style: italic }
-#tpLegendCol1 { padding-left: 1px}
-#tpLegendCol2 { float: right; padding-right: 2px}
+#tpLegendCol1 { padding-left: 1px; vertical-align: middle}
+#tpLegendCol2 { float: right; padding-right: 2px; padding-top:2px}
 .tpLegendSelect { outline: 2px solid black }
 .tpLegendLabel { display:inline; user-select: none; }
 /*.tpLegendCount { display:inline-block; position: absolute; right: 4px; color: #888} */
@@ -130,6 +120,14 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 .tpLegend .tpLegendCheckbox { margin-right: 2px; margin-top: 2px}
 .tpGrey { color: #bbb }
 
+#tpLegendColorChecked,
+#tpLegendAll,
+#tpLegendNone,
+#tpLegendInvert,
+#tpLegendNotNull {
+  font-size: 14px;
+  margin: 1px 1px;
+} 
 
 .ui-helper-reset { font-size: 12px}
 .ui-tabs { padding: 0 }

{cellbrowser-1.2.15.post0.dev8 → cellbrowser-1.2.17}/src/cbPyLib/cellbrowser/cbWeb/js/cbData.js

@@ -106,13 +106,14 @@ var cbUtil = (function () {
                 onSuccess(data);
             },
             error : function() {
-                if (!silent)
+                if (!silent) {
                     if (url.search("dataset.json")>-1)
                         alert("Could not find a dataset at "+url+". If you are sure that the link is correct, please "+
                             "contact the administrator of this server, "+
                             "or cells@ucsc.edu if this is running at UCSC. ");
                     else
                         alert("Could not load "+url);
+                }
                 onSuccess(null);
             }
         });
@@ -440,6 +441,11 @@ function CbDbFile(url) {
             }
         }
 
+        function gotMatrix(data) {
+            matrixIndex = data; 
+            gotOneFile();
+        }
+
         // load config and call onDone
         var dsUrl = cbUtil.joinPaths([this.url, "dataset.json"]);
         // deactivate the cache - this is a small file that users typically change often
@@ -452,7 +458,7 @@ function CbDbFile(url) {
         if (self.name!='') {
             // start loading gene offsets in the background now, because this takes a while
             var osUrl = cbUtil.joinPaths([this.url, "exprMatrix.json"]);
-            cbUtil.loadJson(osUrl, function(data) { matrixIndex = data; gotOneFile();}, true);
+            cbUtil.loadJson(osUrl, gotMatrix, true);
         } else {
             gotOneFile();
         }
@@ -765,29 +771,34 @@ function CbDbFile(url) {
         /* supports NaN special values */
         var breaks = [];
 
+	// remove the Nan values - XX REVISIT
+	for (let i = 0; i < arr.length; i++) {
+	    if (Number.isNaN(arr[i])) {
+	       arr[i] = -Infinity;
+	    }
+	}
+
         // sort expression values into a new array
         var arrSorted = arr.slice(); // slice() = "make copy"
         arrSorted.sort();
 
-        var pos = 0;
-        if (arrSorted[0] == bin0Val) { // skip all bin0Val and remember position
-            var zeros = 0;
+        var minPos = 0;
+        if (arrSorted[0] == bin0Val) { // do we have any values in bin0? -> skip them and keep their position
             for (var i = 0, I = arrSorted.length; i < I; i++) {
                 if (arrSorted[i] > bin0Val) {
-                    pos = i;
+                    minPos = i;
                     break;
                 }
-                zeros += 1;
             }
         }
-        var minVal = arrSorted[pos];
+        var minVal = arrSorted[minPos];
         // calculate optimal bin size in numbers of cells
-        var desiredBinSize = Math.floor((arrSorted.length - pos) / (maxBinCount - breaks.length));
+        var desiredBinSize = Math.floor((arrSorted.length - minPos) / (maxBinCount - breaks.length));
         var currentCount = 0;
-        var binMin = arrSorted[pos];
+        var binMin = arrSorted[minPos];
         var binMax;
         var lastValue;
-        for (var i = pos, I = arrSorted.length; i < I; i++) {
+        for (var i = minPos, I = arrSorted.length; i < I; i++) {
             // determine if current value can be used as a break
             // i.e. it is different from the previous
             var isBreak = false;
@@ -816,16 +827,19 @@ function CbDbFile(url) {
 
         var binInfo = [];
 
-        var bin0MinMax = "Unknown";
+        var bin0MinMax = "Unknown"; // meta data often has empty string = "Unknown"
         if (bin0Val === 0) {
             bin0MinMax = 0;
         }
+        if (bin0Val === FLOATNAN) { // this can only happen for expression matrices with "NAN" values in them
+            bin0MinMax = "NaN";
+        }
         binInfo.push([bin0MinMax, bin0MinMax, binCounts[0]]);
 
         var idx = binCounts[0];
         for (let i=0; i < breaks.length; i++) {
             // use sorted array of expression values
-            // to get more accurate values
+            // to get the exact break values
             var binMin = arrSorted[idx];
             var binCount = binCounts[i+1];
             idx += binCount - 1;
@@ -1008,11 +1022,13 @@ function CbDbFile(url) {
             else
                 geneDesc = geneDescs.join("; ");
 
-            // specVal is the value for a special bin, usually 0
+            // specVal is the value for the first bin, usually 0. But can also be -Infinity
             var specVal = 0;
             var matrixMin = self.getMatrixMin();
             if (matrixMin < 0)
-                specVal = null;
+                specVal = null; // null = no special bin handling at all
+            if (matrixMin === FLOATNAN)
+                specVal = FLOATNAN;
 
             let newArr = [];
             if (updateOp) {
@@ -1023,8 +1039,12 @@ function CbDbFile(url) {
                         newArr = cbUtil.arrAddMult(self.currExprArr, arrs);
                     else
                         newArr = cbUtil.arrSubMult(self.currExprArr, arrs);
-            } else
-                newArr = sumAllArrs(ArrType, arrs);
+            } else {
+                if (arrs.length===1)
+                    newArr = arrs[0];
+                else
+                    newArr = sumAllArrs(ArrType, arrs);
+            }
 
             var discFunc = null;
             if (strategy==="range")
@@ -1682,6 +1702,8 @@ function CbDbFile(url) {
        var matrixMin = 0;
        if ("_range" in validNames)
            matrixMin = validNames["_range"][0];
+       if (matrixMin === null)
+           matrixMin = FLOATNAN;
         return matrixMin;
     }