cellbrowser 1.2.17.2__tar.gz → 1.2.18__tar.gz

{cellbrowser-1.2.17.2/src/cbPyLib/cellbrowser.egg-info → cellbrowser-1.2.18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.17.2
+Version: 1.2.18
 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-1.2.17.2 → cellbrowser-1.2.18}/README.rst

@@ -64,6 +64,7 @@ Many labs host their data at cells.ucsc.edu by sending it to us, but some groups
 * 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/
+* Alex Lemonade Stand Foundation, only requires email, https://scpca.alexslemonade.org/visualize
 
 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:
 

{cellbrowser-1.2.17.2 → cellbrowser-1.2.18}/src/cbPyLib/cellbrowser/R/cellbrowser.R

@@ -1,6 +1,110 @@
 # Build a UCSC cell browser website from a \code{Seurat} object
 #
 NULL
+
+#' Convert a \code{SpatialExperiment} object to a \code{Seurat} object
+#'
+#' Detects whether the object is a Visium or Xenium experiment based on the
+#' spatial coordinate column names, then dispatches to the appropriate helper.
+#' Spatial coordinates are stored as a dimensionality reduction named "spatial"
+#' so that \code{ExportToCellbrowser} exports them as a layout.
+#'
+#' @param spe A \code{SpatialExperiment} object
+#' @return A \code{Seurat} object
+#'
+SpatialExperimentToSeurat <- function(spe) {
+    if (!requireNamespace("SpatialExperiment", quietly = TRUE)) {
+        stop("Package 'SpatialExperiment' is required to convert SpatialExperiment objects. ",
+             "Install with: BiocManager::install('SpatialExperiment')")
+    }
+    coord_cols <- colnames(SpatialExperiment::spatialCoords(spe))
+    if (all(c("x_centroid", "y_centroid") %in% coord_cols)) {
+        message("Detected Xenium SpatialExperiment")
+        return(.xeniumSpeToSeurat(spe))
+    } else {
+        message("Detected Visium SpatialExperiment")
+        return(.visiumSpeToSeurat(spe))
+    }
+}
+
+.xeniumSpeToSeurat <- function(spe) {
+    counts_mat    <- SummarizedExperiment::assay(spe, "counts")
+    metadata      <- SummarizedExperiment::colData(spe)
+    coords        <- SpatialExperiment::spatialCoords(spe)
+
+    # Xenium cell IDs contain special characters; sanitize with make.names()
+    colnames(counts_mat)  <- make.names(colnames(counts_mat))
+    metadata_df           <- as.data.frame(metadata)
+    rownames(metadata_df) <- make.names(rownames(metadata_df))
+    # SPE Xenium coords have no rownames; assign from original cell names
+    coords_df             <- as.data.frame(coords)
+    rownames(coords_df)   <- make.names(colnames(spe))
+
+    seurat_obj <- CreateSeuratObject(counts = counts_mat)
+    seurat_obj@meta.data <- cbind(
+        seurat_obj@meta.data,
+        metadata_df[rownames(seurat_obj@meta.data), ]
+    )
+
+    seurat_obj@meta.data$x_centroid <- coords_df[rownames(seurat_obj@meta.data), "x_centroid"]
+    seurat_obj@meta.data$y_centroid <- coords_df[rownames(seurat_obj@meta.data), "y_centroid"]
+
+    spatial_mat <- as.matrix(seurat_obj@meta.data[, c("x_centroid", "y_centroid")])
+    colnames(spatial_mat) <- c("spatial_1", "spatial_2")
+    seurat_obj[["spatial"]] <- CreateDimReducObject(
+        embeddings = spatial_mat, key = "spatial_", assay = "RNA"
+    )
+
+    seurat_obj <- NormalizeData(seurat_obj)
+    seurat_obj <- FindVariableFeatures(seurat_obj)
+    seurat_obj <- ScaleData(seurat_obj)
+    seurat_obj <- RunPCA(seurat_obj)
+
+    message("Xenium conversion complete: ", ncol(seurat_obj), " cells, ", nrow(seurat_obj), " genes")
+    return(seurat_obj)
+}
+
+.visiumSpeToSeurat <- function(spe) {
+    counts_mat <- SummarizedExperiment::assay(spe, "counts")
+    coords     <- SpatialExperiment::spatialCoords(spe)
+    metadata   <- SummarizedExperiment::colData(spe)
+
+    seurat_obj <- CreateSeuratObject(
+        counts    = counts_mat,
+        meta.data = as.data.frame(metadata)
+    )
+
+    # Try direct barcode matching first; fall back to stripping sample suffixes
+    # (e.g. "ACGTACGT_sample1" in the Seurat object vs "ACGTACGT" in the SPE)
+    coords_df <- as.data.frame(coords)
+    if (all(rownames(seurat_obj@meta.data) %in% rownames(coords_df))) {
+        matched_coords <- coords_df[rownames(seurat_obj@meta.data), ]
+    } else {
+        message("Direct barcode matching failed; retrying with suffix stripping")
+        cell_prefixes  <- sub("_.*", "", rownames(seurat_obj@meta.data))
+        matched_coords <- coords_df[cell_prefixes, ]
+        if (anyNA(matched_coords[, 1]))
+            warning("Some spatial coordinates could not be matched to cell barcodes")
+    }
+
+    seurat_obj@meta.data$imagerow <- matched_coords[, 1]
+    seurat_obj@meta.data$imagecol <- matched_coords[, 2]
+
+    spatial_mat <- as.matrix(seurat_obj@meta.data[, c("imagecol", "imagerow")])
+    colnames(spatial_mat) <- c("spatial_1", "spatial_2")
+    seurat_obj[["spatial"]] <- CreateDimReducObject(
+        embeddings = spatial_mat, key = "spatial_", assay = "RNA"
+    )
+
+    seurat_obj <- NormalizeData(seurat_obj)
+    seurat_obj <- FindVariableFeatures(seurat_obj)
+    seurat_obj <- ScaleData(seurat_obj)
+    seurat_obj <- RunPCA(seurat_obj)
+
+    message("Visium conversion complete: ", ncol(seurat_obj), " cells, ", nrow(seurat_obj), " genes")
+    return(seurat_obj)
+}
+
 #' used by ExportToCellbrowser:
 #' Return a matrix object from a Seurat object or show an error message
 #'
@@ -12,7 +116,12 @@ findMatrices = function(object, slotNames ) {
   slotMatrices = list()
   slots <- list()
   for (slotName in slotNames) {
-      mat <- GetAssayData(object = object, slot = slotName)
+      # work around the pointless deprecation warning which triggers errors in Seurat5/R4.1 installs
+      if (packageVersion("Seurat") >= "5.0.0") {
+          mat <- LayerData(object = object, layer = slotName)
+        } else {
+          mat <- GetAssayData(object = object, slot = slotName)
+      }
       if (slotName == "scale.data")
           slotName <- "scale" #  dots in filenames are not good
       # do not use any prefixes if we export just a single matrix (stay compatible with old code)

{cellbrowser-1.2.17.2 → cellbrowser-1.2.18}/src/cbPyLib/cellbrowser/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-05-01T08:30:24-0700",
- "dirty": false,
+ "date": "2026-06-04T08:52:42-0700",
+ "dirty": true,
  "error": null,
- "full-revisionid": "1a6a9ab68b092f7e8817e346ddb0bef41da4dfbf",
- "version": "1.2.17.2"
+ "full-revisionid": "c09cf26bfbea561975af659004344a386b68819f",
+ "version": "1.2.18"
 }
 '''  # END VERSION_JSON
 

{cellbrowser-1.2.17.2 → cellbrowser-1.2.18}/src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css

@@ -1,7 +1,7 @@
 /* tsneViewer.js class definitions */
 /* * {padding: 0; margin: 0} */ /* important, otherwise precise placement is impossible */ 
 /* body { font-family: Roboto, sans-serif } */
-body { font-family: Arial,Helvetica,sans-serif; overflow:hidden; line-height:1.0}
+body { font-family: Arial,Helvetica,sans-serif; line-height:1.0; overflow:hidden }
 canvas { user-select: none }
 
 section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
@@ -49,7 +49,10 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 }
 
 .tpTitle {
+        position: absolute;
         z-index: 100;
+        border-radius: 3px;
+        padding: 2px 4px;
 }
 
 .tpGeneExprCombo {
@@ -83,29 +86,32 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
     display : block;
     position : absolute;
     font-size : 16px;
+    font-family: Arial, Helvetica, sans-serif;
     color: white;
     text-shadow:
-       1px 1px 0 #000,
-     -1px -1px 0 #000,  
-      1px -1px 0 #000,
-      -1px 1px 0 #000,
-       1px 1px 0 #000;
+       1px 1px 2px rgba(0,0,0,0.8),
+      -1px -1px 2px rgba(0,0,0,0.8),
+       1px -1px 2px rgba(0,0,0,0.8),
+      -1px  1px 2px rgba(0,0,0,0.8);
 }
 
 .sliderContainer {
-        position : absolute;
+        position: absolute;
         display: grid;
-        grid-template-columns: 45px 120px 15px;
-        background: rgba(255,255,255,0.5);
+        grid-template-columns: 45px 120px 20px;
+}
+#mpSliderDiv {
+        padding: 2px 6px 0px 6px;
 }
 
 .sliderLabel {
     font-size: 11px;
     z-index: 10;
     font-weight: bold;
+    background: transparent;
 }
 
-.tpLegend { font-size:13px; /* border: 2px solid transparent; */ cursor:default; word-wrap: break-word; clear:both}
+.tpLegend { font-size:13px; /* border: 2px solid transparent; */ cursor:default; clear:both; display:grid; grid-template-columns:auto auto 1fr auto; column-gap:2px; }
 .tpLegendHl { background-color: #ccc; color: black; }
 .tpHint { font-weight:normal; line-height:1.4; font-size: 80%; margin-top:4px}
 #tpLegendHeader { background-color:#eee; color: #777; margin-top: 2px}
@@ -114,10 +120,10 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 #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; }
+.tpLegendLabel { user-select: none; overflow-wrap: break-word; min-width: 0; }
 /*.tpLegendCount { display:inline-block; position: absolute; right: 4px; color: #888} */
-.tpLegendCount { display:inline-block; float: right; color: #888} 
-.tpLegend .tpLegendCheckbox { margin-right: 2px; margin-top: 2px}
+.tpLegendCount { color: #888; white-space: nowrap; align-self: end; padding-left: 4px; }
+.tpLegend .tpLegendCheckbox { margin-right: 2px; margin-top: 2px; align-self: start; }
 .tpGrey { color: #bbb }
 
 #tpLegendColorChecked,
@@ -129,6 +135,21 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
   margin: 1px 1px;
 } 
 
+.mpFlipbookLabel {
+        font-weight:bold;
+}
+
+#mpFlipbookCont {
+        background: rgba(255,255,255,0.65);
+        padding: 6px 12px 12px;
+        border-radius: 4px;
+        width: auto !important;
+        right: 12px;
+}
+#mpFlipbookCont #mpFlipbook {
+        width: 100% !important;
+}
+
 .ui-helper-reset { font-size: 12px}
 .ui-tabs { padding: 0 }
 .ui-tabs { padding: 0 }
@@ -143,9 +164,9 @@ 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; border-radius: 4px; padding-top: 4px }
+#tpButtonInfo { height: 24px; border-radius: 4px; padding-top: 3px }
 .tpDialogInput { margin-left: 12px; margin-top: 5px; margin-bottom: 12px; }
-#tpDialog { z-index: 1001; }}
+#tpDialog { z-index: 1001; }
 
 .tpIconButton { 
         padding: 1px 2px 1px 2px; 
@@ -157,6 +178,7 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 
 .tpRibbonButton {
         background-color: #ccc;
+        color: #333;
         padding:  1px 2px 1px 2px; 
         border-radius: 4px;
         height: 24px;
@@ -203,7 +225,6 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 .tooltip .tooltip-inner { 
         min-width: 220px; 
         border-radius: 0; 
-        background-opacity: 50%;
         text-align: left
 }
 
@@ -256,13 +277,58 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
         padding-left:1px; 
         padding-right:1px; 
         border: 1px solid #AAA;
-        background: #F6;
+        background: #f6f6f6;
         /*color:#AAAAAA; */
         display: inline-block;
 }
 
-.tpGeneBarCellSelected { 
-        outline: 1px solid black 
+.tpGeneBarCellSelected {
+        outline: 1px solid black
+}
+
+.tpMarkerCellTypeItem {
+        cursor: pointer;
+        padding: 2px 4px;
+        font-size: 12px;
+        border-bottom: 1px solid #eee;
+}
+
+.tpMarkerCellTypeItem:hover {
+        background-color: #e8f0fe;
+}
+
+.tpMarkerBrowseTissue {
+        margin-bottom: 2px;
+}
+
+.tpMarkerBrowseTissueSummary {
+        cursor: pointer;
+        font-size: 12px;
+        font-weight: bold;
+        padding: 3px 4px;
+        background-color: #f0f0f0;
+        border-radius: 2px;
+        user-select: none;
+}
+
+.tpMarkerBrowseTissueSummary:hover {
+        background-color: #e0e0e0;
+}
+
+.tpMarkerBrowseCt {
+        cursor: pointer;
+        padding: 2px 4px 2px 12px;
+        font-size: 12px;
+        border-bottom: 1px solid #f0f0f0;
+}
+
+.tpMarkerBrowseCt:hover {
+        background-color: #e8f0fe;
+}
+
+.tpMarkerBrowseCtSelected {
+        background-color: #d0e4fc;
+        font-weight: bold;
 }
 
 #tpPeakListTitle { 
@@ -296,7 +362,15 @@ input[type=checkbox], input[type=radio] {
 }
 
 
-.tpSidebarHeader { font-weight: bold; padding-left: 4px; font-size: 16px; padding-top: 4px; height: 25px; background-color: white; text-align: center}
+.tpSidebarHeader { 
+        font-weight: bold; 
+        padding-left: 4px; 
+        font-size: 16px; 
+        padding-top: 4px; 
+        height: 25px; 
+        background-color: white; 
+        text-align: center
+}
 
 #tpLeftSidebar { 
         border-right: 1px solid #D7D7D7; 
@@ -327,10 +401,13 @@ input[type=checkbox], input[type=radio] {
         overflow-y: scroll;
 }
 
-#tpLeftTabs { 
-        border: 0; 
+#tpLeftTabs {
+        border: 0;
         height: 100%;
 }
+#tpLeftTabs .ui-tabs-nav li {
+        margin: 0 2px 0 0;
+}
 
 #tpGeneTab, #tpAnnotTab, #tpLayoutTab { 
         border-top: 1px solid #AAA;
@@ -351,6 +428,7 @@ input[type=checkbox], input[type=radio] {
 .tpMetaHistLabel { text-decoration: underline; color: blue }
 .tpMetaValue { height: 1.3em; padding-left: 3px; background-color:#EEE; }
 .tpMetaSelect { outline: 2px solid black; background-color: #DEDEDE }
+.tpMetaLabelSelect { outline: 2px solid black; background-color: #DEDEDE }
 .tpMetaValueSelect { background-color: #CCC}
 .tpMetaPerc { color:grey; float:right }
 .tpMetaSpark { float:right }
@@ -367,16 +445,45 @@ 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 }
 
-.tpButtonInactive { background-color: #EEE; user-select: none; color:#AAA; cursor:default}
+.tpButtonInactive { 
+        background-color: #EEE; 
+        user-select: none; 
+        color:#AAA; 
+        cursor:default;
+}
 
-.tpMenu { z-index: 999; background: white; display:none; position:absolute}
+.tpMenu { 
+        z-index: 999; 
+        background: white; 
+        display:none; 
+        position:absolute;
+}
 
-.sp-replacer { height: 17px; width: 18px; border: none; padding: 0px; margin-right: 5px; background-color: white; vertical-align: top }
+.sp-replacer { 
+        height: 17px; 
+        width: 18px; 
+        border: none; 
+        padding: 0px; 
+        margin-right: 5px; 
+        background-color: white; 
+        vertical-align: top;
+}
 .sp-preview { height: 17px; width: 18px; border: none }
 .sp-dd { line-height: 11px; display:none }
 
@@ -387,7 +494,7 @@ button { line-height: 12px }
 /* bootstraps badges are too dark */
 .list-group-item.active>.badge { background-color: darkgrey; color:white }
 /* bootstrap's small buttons have a lot of padding, for the toolbar, that's too much */
-.noPad {padding:0 2 0 2}
+.noPad {padding:0 2px 0 2px}
 
 /* make the navbar dividers smaller */
 .half-rule { 
@@ -397,7 +504,10 @@ button { line-height: 12px }
     margin-bottom: 0;
 }
 
-#tpToolBar { margin-left: 5px; margin-top: 1px}
+#tpToolBar { margin-left: 5px; margin-top: 1px; display: flex; align-items: center; }
+#tpToolBar button, #tpToolBar a.ui-button { margin-right: 0; vertical-align: middle; }
+#tpClusterMarkersBtn { padding-left: 8px; padding-right: 22px; position: relative; }
+#tpClusterMarkersBtn::after { content: "\25BE"; position: absolute; right: 7px; top: 50%; transform: translateY(-50%); line-height: 1; }
 
 #tpCanvas { }
 
@@ -459,7 +569,7 @@ button { line-height: 12px }
 .nav-tabs > li.active > a { 
         background-color: transparent; 
         border:0;
-        color : black;
+        color: black;
 }
 
 .gradientBackground { background-color: #f6f6f6 }
@@ -596,3 +706,6 @@ th[role=columnheader]:not(.no-sort):hover:after {
   /* Support for IE. */
   font-feature-settings: 'liga';
 }
+/* dataset search result highlighting */
+.tpDatasetLabel mark { background: #fff176; color: inherit; padding: 0 1px; border-radius: 2px; }
+.list-group-item.active .tpDatasetLabel mark { background: #ffe57f; }