cellbrowser - npm Package Compare versions

Comparing version 1.2.15.post0.dev8 to 1.2.16

PKG-INFO

 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.15.post0.dev8
+Version: 1.2.16
 Summary: UCSC Cellbrowser, an interactive browser for single cell data. Includes converters and basic pipelines for text files, Seurat, Scanpy and Cellranger.
@@ -5,0 +5,0 @@ Home-page: https://github.com/maximilianh/cellBrowser

README.rst

@@ -15,4 +15,14 @@ .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
 
-To look at a list of selected single cell datasets, see http://cells.ucsc.edu
+Here are a few datasets that demonstrate these features:
 
+- A simple gene expression dataset: https://cells.ucsc.edu/?ds=cortex-dev
+- 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
+- Cell trajectories from monocle https://cells-test.gi.ucsc.edu/?ds=pre-postnatal-cortex+ex-neu+rna
+- 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 > 200 single cell datasets, see http://cells.ucsc.edu
+
 To setup your own cell browser, from Cellranger, Seurat, Scanpy or text files 
@@ -19,0 +29,0 @@ (tsv/csv), or just a single cell expression matrix, read the documentation

src/cbPyLib/cellbrowser.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.15.post0.dev8
+Version: 1.2.16
 Summary: UCSC Cellbrowser, an interactive browser for single cell data. Includes converters and basic pipelines for text files, Seurat, Scanpy and Cellranger.
@@ -5,0 +5,0 @@ Home-page: https://github.com/maximilianh/cellBrowser

src/cbPyLib/cellbrowser/_version.py

@@ -11,7 +11,7 @@
 {
- "date": "2025-05-22T14:10:47-0700",
+ "date": "2025-11-12T13:17:35-0800",
  "dirty": false,
  "error": null,
- "full-revisionid": "ebe2e27cb09c7f85bdbfee91093a58c64c8ed1b9",
- "version": "1.2.15.post0.dev8"
+ "full-revisionid": "9d80bedf1b39a0e74cf2e6f9f1481d6b6a66c9cc",
+ "version": "1.2.16"
 }
@@ -18,0 +18,0 @@ '''  # END VERSION_JSON

src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css

@@ -72,12 +72,2 @@ /* tsneViewer.js class definitions */
 
-#tpLegendColorChecked,
-#tpLegendAll,
-#tpLegendNone,
-#tpLegendInvert,
-#tpLegendNotNull {
-  font-size: 13px;
-  margin-right: 2px;
-  margin-bottom: 2px;
-}
-
 .tpDatasetPane { 
@@ -121,8 +111,8 @@ padding: 5px !important;
 .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 }
@@ -135,2 +125,10 @@ .tpLegendLabel { display:inline; user-select: none; }
 
+#tpLegendColorChecked,
+#tpLegendAll,
+#tpLegendNone,
+#tpLegendInvert,
+#tpLegendNotNull {
+  font-size: 14px;
+  margin: 1px 1px;
+} 
 
@@ -137,0 +135,0 @@ .ui-helper-reset { font-size: 12px}

src/cbPyLib/cellbrowser/convert.py

@@ -12,2 +12,3 @@ # various format converters for single cell data:
 from .cellbrowser import copyFileIfDiffSize
+from .cellbrowser import generateQuickGenes
 
@@ -33,2 +34,3 @@ from os.path import join, basename, dirname, isfile, isdir, relpath, abspath, getsize, getmtime, expanduser
     reorder - reorder the meta fields
+    quickgenes - make quickgenes.tsv from markers.tsv in current directory
 
@@ -69,3 +71,3 @@ Examples:
 
-    if len(args)<=1:
+    if len(args)<=1 and not (len(args)!=0 and args[0]=="quickgenes"):
         cbToolCli_parseArgs(showHelp=True)
@@ -76,3 +78,3 @@ sys.exit(1)
 
-    cmds = ["mtx2tsv", "matCatCells", "matCatGenes" "metaCat", "reorder", "cxg"]
+    cmds = ["mtx2tsv", "matCatCells", "matCatGenes" "metaCat", "reorder", "cxg", "quickgenes"]
 
@@ -130,2 +132,6 @@ if cmd=="mtx2tsv":
         metaCat(inFnames, outFname, options)
+
+    elif cmd=="quickgenes":
+        generateQuickGenes(".")
+
     else:
@@ -132,0 +138,0 @@ errAbort("Command %s is not a valid command. Valid commands are: %s" % (cmd, ", ".join(cmds)))

src/cbPyLib/cellbrowser/geneinfo.py

@@ -235,4 +235,16 @@ # annotate a list of gene IDs with links to various external databases
             headers.append("_geneLists")
+
+            # lineFileNextRow makes some changes to seurat headers that we need to undo
+            if headers[0] == "rowName":
+                headers[0] = ''
+            if headers[3] == "pct_1":
+                headers[3] = "pct.1"
+            if headers[4] == "pct_2":
+                headers[4] = "pct.2"
             yield headers
         sym = row[1]
+        isSeurat = False
+        if sym.isnumeric(): # if column 2 is only a number, it's probably a seurat file
+            sym = row[0] # gene symbol is in column 1
+            isSeurat = True
         if "|" in sym: # marker gene lists can carry geneId|symbol, strip the symbol in this case and re-convert below
@@ -306,3 +318,6 @@ sym = sym.split("|")[0]
         row = list(row)
-        row[1] = sym # in case the original ID was a geneID, not a symbol
+        if isSeurat:
+            row[0] = sym # for seurat files, column 1 is the gene
+        else:
+            row[1] = sym # in case the original ID was a geneID, not a symbol
 
@@ -309,0 +324,0 @@ row.append(hprdClass)

src/cbPyLib/cellbrowser/genes.py

@@ -49,2 +49,3 @@ # functions to guess the gene model release given a list of gene IDs
     %prog allSyms human # build big geneId -> symbol table from all 
+    %prog json ce11 wormbase235 # build JSON file from a .bed.gz file - only needed for model organisms
     """)
@@ -220,3 +221,3 @@
         db = "hg19"
-    url = "https://hgdownload.cse.ucsc.edu/goldenPath/%s/database/wgEncodeGencodeAttrsV%s.txt.gz" %  (db, release)
+    url = "https://hgdownload.gi.ucsc.edu/goldenPath/%s/database/wgEncodeGencodeAttrsV%s.txt.gz" %  (db, release)
     logging.info("Downloading %s" % url)
@@ -248,3 +249,3 @@ doneIds = set()
 
-    url = "http://hgdownload.cse.ucsc.edu/goldenPath/%s/database/wgEncodeGencodeCompV%s.txt.gz" % (db, release)
+    url = "http://hgdownload.gi.ucsc.edu/goldenPath/%s/database/wgEncodeGencodeCompV%s.txt.gz" % (db, release)
     logging.info("Downloading %s" % url)
@@ -380,6 +381,6 @@ geneToTransList = defaultdict(list)
     sep = "\n"
-    urls = [("hg38", "https://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/"),
-            ("mm10", "https://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/"),
-            ("mm39", "https://hgdownload.cse.ucsc.edu/goldenPath/mm39/database/"),
-            ("hg19", "https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/")
+    urls = [("hg38", "https://hgdownload.gi.ucsc.edu/goldenPath/hg38/database/"),
+            ("mm10", "https://hgdownload.gi.ucsc.edu/goldenPath/mm10/database/"),
+            ("mm39", "https://hgdownload.gi.ucsc.edu/goldenPath/mm39/database/"),
+            ("hg19", "https://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/")
             ]
@@ -514,3 +515,3 @@
     " convert BED file to more compact json file: chrom -> list of (start, end, strand, gene) "
-    geneToSym = readGeneSymbols(geneIdType)
+    transToSym = readGeneSymbols(geneIdType)
 
@@ -520,17 +521,24 @@ # index transcripts by gene
     for row in iterBedRows(db, geneIdType):
-        chrom, start, end, geneId, score, strand = row[:6]
-        sym = geneToSym[geneId]
+        chrom, start, end, transId, score, strand = row[:6]
+        if not transId in transToSym:
+            logging.warn("%s does not have a gene symbol" % transId)
+            sym = transId
+        else:
+            sym = transToSym[transId]
+            logging.debug("Mapping %s to symbol %s" % (transId, sym))
         start = int(start)
         end = int(end)
         transLen = end-start
-        rawGeneId = geneId.split(".")[0] # for lookups, we hopefully will never need the version ID...
-        fullGeneId = rawGeneId+"|"+sym
-        bySym[fullGeneId].setdefault(chrom, []).append( (transLen, start, end, strand, geneId) )
+        rawTransId = transId
+        if rawTransId.startswith("EN") or rawTransId.startswith("NM_"):
+            rawTransId = transId.split(".")[0] # for lookups, we hopefully will never need the version ID...
+        fullTransId = rawTransId+"|"+sym
+        bySym[sym].setdefault(chrom, []).append( (transLen, start, end, strand, fullTransId) )
 
     symLocs = defaultdict(list)
-    for geneId, chromDict in bySym.items():
+    for sym, chromDict in bySym.items():
         for chrom, transList in chromDict.items():
             transList.sort(reverse=True) # take longest transcript per chrom
             _, start, end, strand, transId = transList[0]
-            symLocs[chrom].append( (start, end, strand, geneId) )
+            symLocs[chrom].append( (start, end, strand, transId) )
 
@@ -624,7 +632,8 @@ sortedLocs = {}
 
-    elif command=="json": # undocumented
-        db, geneType, outFname = args[1:]
-        bedToJson(db, geneType, outFname)
+    elif command=="json":
+        db, geneType = args[1:]
+        jsonFname = getStaticPath(getGeneJsonPath(db, geneType))
+        bedToJson(db, geneType, jsonFname)
     else:
         errAbort("Unrecognized command: %s" % command)
 

src/cbPyLib/cellbrowser/hubmaker.py

@@ -674,8 +674,6 @@ # create a track hub from an expression matrix
     " write the barChart tdb stanza "
-    stepSize = 1.0 / len(clusterNames)
     colorCodes = []
-    x = 0
-    while x < 1.0:
+    for i in range(len(clusterNames)):
+        x = i / len(clusterNames)
         colorCodes.append(colorsys.hsv_to_rgb(x, 1.0, 1.0))
-        x+=stepSize
 
@@ -682,0 +680,0 @@ hexCodes = [toHex(x) for x in colorCodes]

src/cbPyLib/cellbrowser/R/cellbrowser.R

@@ -90,2 +90,24 @@ # Build a UCSC cell browser website from a \code{Seurat} object
         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); 
@@ -104,8 +126,15 @@ if (is.null(img)) {
         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)
@@ -420,5 +449,8 @@ conf <- sprintf(
         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)
         }
@@ -425,0 +457,0 @@ markers <- FindAllMarkers(

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