cellbrowser 1.2.3__tar.gz → 1.2.4__tar.gz

{cellbrowser-1.2.3/src/cbPyLib/cellbrowser.egg-info → cellbrowser-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.3
+Version: 1.2.4
 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-1.2.3 → cellbrowser-1.2.4}/README.rst

@@ -5,8 +5,12 @@ UCSC Single Cell Browser
 ========================
 
 The UCSC Cell Browser is a viewer for single cell data. You can click on and
-hover over cells to get meta information, search for genes to color on and
-click clusters to show cluster-specific marker genes. 
+hover over cells to get meta information, select cells to get annotation histograms, 
+make expression violin plots and heatmaps, search for genes to color on and
+click clusters to show cluster-specific marker genes. It supports the usual gene expression plots, ATAC,
+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
 
@@ -57,8 +61,8 @@ ticket system with more features and that a lot of communication with wetlab use
 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.
 
-Additional availability
------------------------
+Install and use
+---------------
 
 * The preferred installation is via pip https://pypi.org/project/cellbrowser/, for documentation see https://cellbrowser.readthedocs.io
 * Bioconda: this tool is available to install via `bioconda <https://bioconda.github.io/recipes/ucsc-cell-browser/README.html>`_. Note that the conda release is usually a bit outdated relative to the pip release, so use pip if possible. If you cannot use pip, please contact us. 
@@ -67,7 +71,7 @@ Additional availability
 * 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 is funded through a supplement to the NHGRI Genome Browser grant.
+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.
 
 This is early research software. You are likely to find bugs. Please open a Github
 ticket or email us at cells@ucsc.edu, we can usually fix them quickly.

{cellbrowser-1.2.3 → cellbrowser-1.2.4}/src/cbPyLib/cellbrowser/R/cellbrowser.R

@@ -46,15 +46,18 @@ saveMatrix <- function(counts, dir, prefix, use.mtx) {
         genesPath <- file.path(dir, paste(prefix, "features.tsv", sep=""))
         barcodesPath <- file.path(dir, paste(prefix, "barcodes.tsv", sep=""))
         message("Writing expression matrix to ", matrixPath)
+        if (class(counts)[1]=="matrix") {
+            counts <- as(counts, "sparseMatrix")
+        }
         writeMM(counts, matrixPath)
         # easier to load if the genes file has at least two columns. Even though seurat objects
         # don't have yet explicit geneIds/geneSyms data, we just duplicate whatever the matrix has now
         write.table(as.data.frame(cbind(rownames(counts), rownames(counts))), file=genesPath, sep="\t", row.names=F, col.names=F, quote=F)
         write(colnames(counts), file = barcodesPath)
         message("Gzipping expression matrix")
-        gzip(matrixPath)
-        gzip(genesPath)
-        gzip(barcodesPath)
+        gzip(matrixPath, overwrite=TRUE)
+        gzip(genesPath, overwrite=TRUE)
+        gzip(barcodesPath, overwrite=TRUE)
   } else {
       # we can write the matrix as a tsv file
       gzPath <- file.path(dir, paste(prefix, "exprMatrix.tsv.gz", sep=""))
@@ -69,6 +72,50 @@ saveMatrix <- function(counts, dir, prefix, use.mtx) {
   }
 }
 
+exportImages <- function(obj, outDir, embeddings.conf) {
+#' used by ExportToCellbrowser:
+#' Write spatial images to outDir
+#'
+#' @param obj The Seurat4 object
+#' @param outDir output directory
+#' @param an array of strings to write into the coords object into the cellbrowser config file
+#'
+    if (length(obj@images)==0)
+        return(embeddings.conf)
+
+    message("Exporting spatial images")
+    require(png)
+    for (name in names(obj@images)) { 
+        message(name); 
+        img = GetImage(obj, mode="raw", image=name); 
+        imgPath <- file.path(outDir, paste0(name, ".jpg"))
+        message("Writing image ", imgPath)
+        #writePNG(img, imgPath);  # JPEG seems like a better choice here, 4x smaller at default quality settings.
+        writeJPEG(img, target=imgPath, quality=0.95); 
+        yMax = dim(img)[1];
+        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")
+
+        write.table(coordsRev, coordsPath, sep="\t", row.names=T, quote=F, col.names=NA)
+        conf <- sprintf(
+         '  {\n    "file": "%s",\n    "shortLabel": "Spatial %s",\n    "flipY":True,\n    "images" : [{"file":"%s"}],\n     "minX":0, "minY":0, "maxX":%d, "maxY":%d\n  }',
+         coordsPath,
+         name,
+         imgPath,
+         xMax,
+         yMax
+        )
+        embeddings.conf <- c(conf, embeddings.conf)
+    }
+    return(embeddings.conf)
+}
+
 #' Export \code{Seurat} objects for UCSC cell browser and stop open cell browser
 #' instances from R
 #'
@@ -119,6 +166,7 @@ saveMatrix <- function(counts, dir, prefix, use.mtx) {
 #' @importFrom reticulate py_module_available import
 #' @importFrom Seurat Project Idents GetAssayData Embeddings FetchData
 #' @importFrom Matrix  writeMM
+#' @importFrom jpeg writeJPEG
 #'
 #' @export
 #'
@@ -195,6 +243,16 @@ ExportToCellbrowser <- function(
             break
         }
     }
+    if (is.null(x = cluster.field)) {
+        message("There is no meta field identical to idents(): using the value of Idents() as a new field 'Cluster'")
+        # create a new meta data field named "Cluster"
+        newDf <- cbind(object@meta.data, Idents(object))
+        # default name is "Idents(object)", not good, let's rename that to "Cluster"
+        names(newDf)[length(newDf)] <- "Cluster"
+        object@meta.data <- newDf
+        cluster.field <- "Cluster"
+    }
+
   } else {
     message("A custom cluster field was specified: ", cluster.field)
     Idents(object) <- object[[cluster.field]]
@@ -206,7 +264,7 @@ ExportToCellbrowser <- function(
 
   if (is.null(x = meta.fields)) {
     meta.fields <- colnames(x = meta)
-    if (length(x = levels(x = idents)) > 1) {
+    if (length(x = levels(x = Idents(object))) > 1) {
       meta.fields <- c(meta.fields, ".ident")
     }
   }
@@ -278,7 +336,7 @@ ExportToCellbrowser <- function(
   embeddings.conf <- c()
   for (embedName in foundEmbedNames) {
       conf <- sprintf(
-        '{"file": "%s.coords.tsv", "shortLabel": "Seurat %1$s"}',
+        '  {"file": "%s.coords.tsv", "shortLabel": "Seurat %1$s"}',
         embedName
       )
       embeddings.conf <- c(embeddings.conf, conf)
@@ -287,7 +345,7 @@ ExportToCellbrowser <- function(
   df <- data.frame(row.names = cellOrder, check.names = FALSE)
   for (field in meta.fields) {
     if (field == ".ident") {
-      df$Cluster <- idents
+      df$Cluster <- Idents(object)
       enum.fields <- c(enum.fields, "Cluster")
     } else {
       name <- meta.fields.names[[field]]
@@ -321,7 +379,7 @@ ExportToCellbrowser <- function(
     file <- NULL
   }
   if (is.null(markers.file) && !skip.markers) {
-    if (length(levels(idents)) > 1) {
+    if (length(levels(Idents(object))) > 1) {
       markers.helper <- function(x) {
         partition <- markers[x,]
 
@@ -391,6 +449,8 @@ ExportToCellbrowser <- function(
     matrixOutPath <- sprintf("%s%smatrix.mtx.gz", firstPrefix, matSep)
   }
 
+  embeddings.conf <- exportImages(object, dir, embeddings.conf)
+
   config <- '# This is a bare-bones cellbrowser config file auto-generated by the command-line tool cbImportSeurat 
 # or directly from R with SeuratWrappers::ExportToCellbrowser().
 # Look at https://github.com/maximilianh/cellBrowser/blob/master/src/cbPyLib/cellbrowser/sampleConfig/cellbrowser.conf

{cellbrowser-1.2.3 → cellbrowser-1.2.4}/src/cbPyLib/cellbrowser/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-05-23T14:12:11-0700",
- "dirty": true,
+ "date": "2024-01-26T10:33:46-0800",
+ "dirty": false,
  "error": null,
- "full-revisionid": "3df4aba4fdc714549c359d83c6fa819021f46281",
- "version": "v1.2.3"
+ "full-revisionid": "79b1a8dc88b82ca35ec995490618ad73697c354f",
+ "version": "v1.2.4"
 }
 '''  # END VERSION_JSON
 

{cellbrowser-1.2.3 → cellbrowser-1.2.4}/src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css

@@ -8,22 +8,56 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 
 #tpExprViewTitle { 
         background-color: #eee;
-        padding: 3px;
+        padding: 5px;
+        height: 25px;
         /*border-bottom: 1px solid black; */
 }
 
 #tpExprView { 
         position: absolute;
         z-index: 100;
-        top: 1%;
-        left: 1%;
         display: block;
         background-color: white;
-        height: 98%;
-        width: 98%;
+        top: 1%;
+        left: 1%;
+        height: 99%;
+        width: 99%;
         border: 1px solid grey;
 }
 
+#tpGeneExprMetaLabel {
+        margin-left: 6px;
+        margin-right: 6px;
+}
+
+#tpExprViewPlot {
+        display:flex;
+        flex-direction: row;
+        flex-flow: wrap;
+        height:100%;
+        padding-top:10px;
+        overflow: scroll;
+}
+
+#tpExprViewContent {
+        padding: 6px;
+        height: 100%;
+}
+
+#tpGeneExprLabel {
+        margin-right: 6px;
+}
+
+.tpGeneExprCombo {
+        margin-left: 6px;
+        margin-right: 6px;
+}
+
+/* selectize dropdown triangle is black by default, make light grey like chosen's triangle */
+.selectize-control.single .selectize-input:after {
+        border-color: #888 transparent transparent transparent;
+}
+
 #tpLegendBar { 
         cursor:default; 
         padding-left: 2px; 
@@ -54,7 +88,20 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
        1px 1px 0 #000;
 }
 
+.sliderContainer {
+        position : absolute;
+        display: grid;
+        grid-template-columns: 45px 120px 15px;
+}
+
+.sliderLabel {
+    font-size: 11px;
+    z-index: 10;
+    font-weight: bold;
+}
+
 .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 }
 #tpLegendTitle { font-weight: bold }
@@ -68,6 +115,7 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 .tpLegend .tpLegendCheckbox { margin-right: 2px; margin-top: 2px}
 .tpGrey { color: #bbb }
 
+
 .ui-helper-reset { font-size: 12px}
 .ui-tabs { padding: 0 }
 .ui-tabs { padding: 0 }
@@ -85,7 +133,28 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 #tpButtonInfo { height: 24px; top: 1px; margin-right: 8px; width: 120px; border-radius: 4px }
 .tpDialogInput { margin-left: 12px; margin-top: 5px; margin-bottom: 12px; }
 
-.tpIconButton { padding: 1px 2px 1px 2px; border-radius: 0; height:28px; width: 28px; cursor: default}
+.tpIconButton { 
+        padding: 1px 2px 1px 2px; 
+        border-radius: 0; 
+        height:28px; 
+        width: 28px; 
+        cursor: default
+}
+
+.tpRibbonButton {
+        padding:  1px 2px 1px 2px; 
+        border-radius: 4px;
+        height: 24px;
+        border: 1px solid #c5c5c5;
+        vertical-align: top;
+        text-align: center;
+        margin-right: 8px;
+        top: 3px;
+        position: relative;
+        padding-left: 4px;
+        padding-right: 4px;
+}
+
 .tpClicked { background-color: #AAA }
 .tpClicked:hover { background-color: #AAA }
 .btn-primary.load-dataset {float: right; margin-left: 10px; color: white; font-size: 12px; margin-top: -4px;}
@@ -109,7 +178,7 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 }
 
 /* modify bootstrap tooltip defaults */
-.tooltip-inner { min-width: 220px; border-radius: 0}
+.tooltip-inner { min-width: 220px; border-radius: 0; background-opacity: 50%}
 
  .ui-widget-header { background: white} 
 .ui-state-active { background: green }
@@ -124,6 +193,19 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
     font-weight: bold;
 }
 
+/* expression progress bar only */
+.ui-progressbar {
+        position: relative;
+}
+.progress-label {
+        position: absolute;
+        left: 50%;
+        top: 4px;
+        font-weight: bold;
+        /*text-shadow: 1px 1px 0 #fff;*/
+}
+
+
 .context-menu-item { 
         font-size: 13px; 
         padding: 3px 
@@ -183,7 +265,7 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 }
 
 input[type=checkbox], input[type=radio] {
-        vertical-align : -2px; // https://stackoverflow.com/a/2806786/233871
+        vertical-align : -2px; /* https://stackoverflow.com/a/2806786/233871 */
 }
 
 
@@ -223,7 +305,7 @@ input[type=checkbox], input[type=radio] {
         height: 100%;
 }
 
-#tpGeneTab, #tpAnnotTab { 
+#tpGeneTab, #tpAnnotTab, #tpLayoutTab { 
         border-top: 1px solid #AAA;
         padding:0;
         padding-top: 5px;
@@ -292,6 +374,25 @@ button { line-height: 12px }
 .tpToolBarItem { display:inline-block; white-space: nowrap }
 .tpToolBarItem > label { margin-right: 7px; display: inline} 
 
+.tpLeftSideItem { 
+        display:inline-block; 
+        white-space: nowrap;
+        width:100%
+}
+.tpLeftSideItem > label { 
+        margin-right: 7px; 
+        display: inline; 
+        display:block; 
+        margin-bottom:8px; 
+        padding-top: 8px;
+        padding-left:4px
+} 
+#tpLayoutCombo_chosen {
+        width:100%;
+        padding-left:4px;
+        padding-right:2px;
+}
+
 .tpCombo { display: inline-block}