fixes maximilianh#56, also adding various redmine fixed found by @mat…

…thewspeir
ucscGenomeBrowser · Dec 6, 2018 · f069571 · f069571
1 parent cf89c61
commit f069571
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Showing 6 changed files with 23 additions and 14 deletions.
diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="cellbrowser",
-    version="0.4.23",
+    version="0.4.24",
     license="GPL 3",
     python_requires='>=2.5',
     author="Maximilian Haeussler",

diff --git a/src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css b/src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css
@@ -24,7 +24,7 @@ canvas { user-select: none }
 .ui-tabs .ui-tabs-panel { padding-top:5px; border:1px solid lightgray !important; padding:0} /* for marker panels */
 .ui-tabs-anchor { padding: 3px !important}
 .ui-tabs .ui-tabs-nav .ui-tabs-anchor { padding: 3px }
-.tab-pane { padding-top: 8px; border: 1px solid lightgrey; padding: 4px }
+.tab-pane { padding: .4em 1em; border: 1px solid lightgrey }
 .ui-corner-all { border-radius: 0px } /* dialogs */
 #tpOpenDatasetButton { border-radius: 4px }
 .ui-menu-item { font-size:13px }

diff --git a/src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js b/src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js
@@ -323,7 +323,7 @@ var tsnePlot = function() {
         var winWidth = window.innerWidth - 0.05*window.innerWidth;
         var winHeight = window.innerHeight - 0.05*window.innerHeight;
         var buttonWidth = 400;
-        var tabsWidth = winWidth - buttonWidth - 50;
+        var tabsWidth = winWidth - buttonWidth - 70;
 
 
         var htmls = [];
@@ -363,15 +363,15 @@ var tsnePlot = function() {
 
         htmls.push("<div class='tab-content'>");
 
-        htmls.push("<div id='pane1' class='tab-pane'>");
+        htmls.push("<div id='pane1' class='tpDatasetPane tab-pane'>");
         htmls.push("<p>Loading abstract...</p>");
         htmls.push("</div>");
 
-        htmls.push("<div id='pane2' class='tab-pane'>");
+        htmls.push("<div id='pane2' class='tpDatasetPane tab-pane'>");
         htmls.push("<p>Loading methods...</p>");
         htmls.push("</div>");
 
-        htmls.push("<div id='pane3' class='tab-pane'>");
+        htmls.push("<div id='pane3' class='tpDatasetPane tab-pane'>");
         htmls.push("<p>Loading data download...</p>");
         htmls.push("</div>");
 
@@ -3607,14 +3607,15 @@ var tsnePlot = function() {
 
         console.log("building marker genes window for "+clusterName);
         var htmls = [];
-        htmls.push("<div id='tpPaneHeader' style='padding:8px'>");
+        htmls.push("<div id='tpPaneHeader' style='padding:0.4em 1em'>");
 
         var buttons = {};
 
         if (tabInfo===undefined || tabInfo.length===0) {
             tabInfo = [];
-            htmls.push("No marker genes are available in this dataset. "
-                "To add marker genes, contact the original author of the dataset and ask them to add "
+            buttons["Close"] = function() { $( this ).dialog( "close" )}; 
+            htmls.push("No marker genes are available in this dataset. " +
+                "To add marker genes, contact the original authors of the dataset and ask them to add " +
                 " them to the cell browser.");
         } else {
             htmls.push("Click gene symbols below to color plot by gene<br>");

diff --git a/src/cbPyLib/cellbrowser/cellbrowser.py b/src/cbPyLib/cellbrowser/cellbrowser.py
@@ -72,11 +72,11 @@
     #  generic igraph neighbor-based layouts
     "fa": "ForceAtlas2",
     "fr": "Fruchterman Reingold",
-    #"grid_fr": "Grid Fruchterman Reingold", # deactivated for now due to https://github.com/igraph/python-igraph/issues/152
+    "grid_fr": "Grid Fruchterman Reingold", # deactivated for now due to https://github.com/igraph/python-igraph/issues/152
     "kk": "Kamadi Kawai",
-    #"lgl": "Large Graph Layout", # looks useless
+    "lgl": "Large Graph Layout", # looks useless
     "drl": "DrL Distributed Recursive Layout",
-    #"rt": "Reingold Tilford tree", # doesn't look useful
+    "rt": "Reingold Tilford tree", # doesn't look useful
 
     # special scanpy layouts
     "tsne" : "t-SNE",
@@ -86,6 +86,8 @@
     "phate" : "PHATE"
 }
 
+recommendedLayouts = ["fa", "fr", "kk", "drl", "tsne", "umap", "pagaFa", "phate"]
+
 metaLabels = {
     "louvain" : "Louvain Cluster",
     "percent_mito" : "Percent Mitochond.",
@@ -3136,7 +3138,7 @@ def checkLayouts(conf):
 
     doLayouts = conf["doLayouts"]
     if doLayouts=="all":
-        doLayouts = list( coordLabels.keys() )
+        doLayouts = recommendedLayouts
 
     for l in doLayouts:
         if l not in coordLabels:

diff --git a/src/cbPyLib/cellbrowser/sampleConfig/scanpy.conf b/src/cbPyLib/cellbrowser/sampleConfig/scanpy.conf
@@ -53,7 +53,9 @@ louvainRes = 1.0
 #     than ‘fr’), ‘kk’ (Kamadi Kawai’, slower than ‘fr’), ‘lgl’ (Large Graph, very
 #     fast), ‘drl’ (Distributed Recursive Layout, pretty fast) and ‘rt’ (Reingold
 #     Tilford tree layout).
-# You can also set doLayouts="all" to generate all possible layouts mentioned above.
+# You can also set doLayouts="all" to generate our favorite layouts, which is
+# everything above except lgl/rt as they do not seem useful or grid_fr which
+# is sometimes tricky to install.
 doLayouts = ["fa", "umap"]
 
 # find top marker genes per cluster?

diff --git a/src/cbPyLib/cellbrowser/seurat.py b/src/cbPyLib/cellbrowser/seurat.py
@@ -153,6 +153,10 @@ def writeSeurat2Script(conf, inData, tsnePath, clusterPath, markerPath, rdsPath,
     # PCA
     cmds.append('print("Running PCA")')
     pcCountConfig = conf.get("pcCount", 30)
+    # see: https://github.com/satijalab/seurat/issues/982
+    # pca = SeuratObj@dr$pca
+    # eigValues = (pca@sdev) ^2 ## 
+    # varExplained = eigValues / sum(eigValues)
     #if pcCountConfig == "auto":
         #cmds.append('sobj <- JackStraw(object = sobj, num.replicate = 100, display.progress = FALSE)')
         #cmds.append('JackStrawPlot(object = sobj, PCs = 1:12)')