Merge branch 'master' of github.com:maximilianh/cellBrowser

Author: maximilianh

src/cbPyLib/cellbrowser/R/ExportToCellbrowser-seurat2.R

@@ -45,8 +45,8 @@ ExportToCellbrowser <- function(
   skip.markers = FALSE,
   all.meta = FALSE
 ) {
-  if (substr(object@version, 1, 1)!='2') { 
-          stop("can only process Seurat2 objects, version of rds is ", object@version) 
+  if (substr(object@version, 1, 1)!='2') {
+          stop("can only process Seurat2 objects, version of rds is ", object@version)
   }
 
   #idents <- FetchData(object,c("ident"))$ident;
@@ -150,23 +150,32 @@ ExportToCellbrowser <- function(
   }
   file <- paste0("markers.", ext)
   fname <- file.path(dir, file)
-  if (is.null(markers.file) & !skip.markers) {
+
+  if (!is.null(markers.file) && !skip.markers) {
+    message("Copying ", markers.file, " to ", fname)
+    file.copy(markers.file, fname)
+  }
+  if (is.null(markers.file) && skip.markers) {
+    file <- NULL
+  }
+  if (is.null(markers.file) && !skip.markers) {
     if (length(levels(idents)) > 1) {
       message("Running FindAllMarkers(), using ROC test, min logfc diff 0.35, and writing top ", markers.n, ", cluster markers to ", fname)
       markers <- FindAllMarkers(object, do.print=TRUE, print.bar=TRUE, test.use="roc", logfc.threshold = 0.35)
-      require(dplyr) # if this fails, install dplyr with install.packages("dplyr")
-      top.markers <- markers %>% group_by(cluster) %>% top_n(markers.n, avg_logFC)
-      write.table(top.markers, fname, quote=FALSE, sep="\t", row.names=FALSE)
+      markers.helper <- function(x) {
+        partition <- markers[x,]
+        ord <- order(partition$p_val_adj < 0.05, -partition$avg_logFC)
+        res <- x[ord]
+        res <- c(res[1:markers.n], rep(NA, length(x) - markers.n))
+        return(res)
+      }
+      markers.order <- ave(rownames(markers), markers$cluster, FUN=markers.helper)
+      top.markers <- markers[markers.order[!is.na(markers.order)],]
+      write.table(top.markers, fname, quote=FALSE, sep="\t", col.names=NA)
     } else {
+      message("No clusters found in Seurat object, so no marker genes can be computed")
       file <- NULL
     }
-  } else if (!skip.markers) {
-    message("Copying ", markers.file, " to ", fname)
-    file.copy(markers.file, fname)
-  }
-  else {
-      message("No marker genes file defined")
-      file <- NULL
   }
 
   if (!is.null(file)) {

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

@@ -33,8 +33,9 @@ canvas { user-select: none }
 .tpIconButton { padding: 1px 2px 1px 2px; border-radius: 0; height:28px; width: 28px; cursor: default}
 .tpClicked { background-color: #AAA }
 .tpClicked:hover { background-color: #AAA }
-.btn-primary.load-dataset {float: right; margin-left: 10px; color: white;}
+.btn-primary.load-dataset {float: right; margin-left: 10px; color: white; font-size: 12px; margin-top: -4px;}
 .list-group-item.active>.btn-primary {color: #337ab7;background-color: #fff;}
+.list-group-item .badge {margin-top: -2px;}
 
 .link { text-decoration: underline; color: #0000EE; cursor: pointer; }
 
@@ -169,7 +170,7 @@ button { line-height: 12px }
 
 /* flying-sheep's suggestions */
 .ui-dialog-titlebar { border: none }
-button.list-group-item { background-color: #EEE }
+a.list-group-item { background-color: #EEE }
 .nav-tabs > li > a { border-top-left-radius: 4px; border-top-right-radius: 4px; background-color: #EEE; padding-left: 10px; padding-right: 10px; padding-top: 4px; padding-bottom:4px}
 .nav-tabs > li.active > a { background-color: #337ab7; color: white; border: 1px solid #EEE }
 /* .nav-tabs > li { background-color: #E9E9E9 } */

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

@@ -336,9 +336,9 @@ var tsnePlot = function() {
         htmls.push("<div class='list-group' style='width:"+buttonWidth+"px'>");
         for (var i = 0; i < gDatasetList.length; i++) {
             var dataset = gDatasetList[i];
-            var line = "<button id='tpDatasetButton_"+i+"' type='button' class='list-group-item' data-datasetid='"+i+"'>"; // bootstrap seems to remove the id
+            var line = "<a id='tpDatasetButton_"+i+"' role='button' class='list-group-item' data-datasetid='"+i+"'>"; // bootstrap seems to remove the id
             htmls.push(line);
-            htmls.push('<a role="button" class="btn btn-primary btn-xs load-dataset">Open dataset</a>')
+            htmls.push('<button type="button" class="btn btn-primary btn-xs load-dataset">Open dataset</button>')
 
             if (dataset.sampleCount!==undefined) {
                 var countDesc = prettyNumber(dataset.sampleCount);
@@ -351,7 +351,7 @@ var tsnePlot = function() {
                 htmls.push("<span class='badge'>"+tag+"</span>");
                 }
             }
-            htmls.push(dataset.shortLabel+"</button>");
+            htmls.push(dataset.shortLabel+"</a>");
             if (db!==null && db.name===dataset.name)
                 activeIdx = i;
         }