FDSTools v1.0.1.dev2

* Samplevis v2.1.2 (additionally):
  * The net effect of the allele calling thresholds (table filtering options)
    is now visualised in the graphs as a dashed vertical red line.
  * Fixed issue with allele calling thresholds not working anymore after having
    used the 'Save page' link in HTML visualisations.

fdstools/__init__.py

@@ -24,7 +24,7 @@ including tools for characterisation and filtering of PCR stutter artefacts and
 other systemic noise, and for automatic detection of the alleles in a sample.
 """
 
-__version_info__ = ('1', '0', '1', 'dev1')
+__version_info__ = ('1', '0', '1', 'dev2')
 __version__ = '.'.join(__version_info__)
 usage = __doc__.split("\n\n\n")
 

fdstools/vis/samplevis/index.html

@@ -35,7 +35,7 @@
         font-size: 1em;
     }
     .icon {
-        padding: 1em;
+        padding: 0em 1em;
         margin-right: .25em;
         background-size: contain;
         background-position: center;
@@ -1403,9 +1403,10 @@ function savePage(){
     var link = document.getElementById("savePageLink");
     if(link.getAttribute("class") == "disabled")
         return false;
+
+    //Get current settings and copy graph spec.
     var rendererName = document.querySelector("input[name=renderer]:checked").value;
     var splitMarkers = document.getElementById("splitmarkers").checked;
-    var x = PAT_LOAD_SCRIPT.exec(pagehtml);
     var graph_specx = JSON.parse(JSON.stringify(graph_spec));
     for(i in graph_specx.signals)
         if(graph_specx.signals[i].name == "filter_marker"){
@@ -1415,28 +1416,11 @@ function savePage(){
     graph_specx.data[0].fdstools_filename = fileName;
     graph_specx.data[0].format = data_format;
     graph_specx.data[0].values = "";
-    var sel = userSelected.map(function(sa){
-        sa._prev = null;
-        sa._id = null;
-        sa.aggr._id = null;
-        sa.rank = null;
-        sa.thedatum = null;
-        return sa;
-    });
-    var desel = userDeselected.map(function(sa){
-        sa._prev = null;
-        sa._id = null;
-        sa.aggr._id = null;
-        sa.rank = null;
-        sa.thedatum = null;
-        return sa;
-    });
+
+    //Gather user-selected and user-deselected alleles.
+    var sel = userSelected.slice();
+    var desel = userDeselected.slice();
     selectedAlleles.forEach(function(sa){
-        sa._prev = null;
-        sa._id = null;
-        sa.aggr._id = null;
-        sa.rank = null;
-        sa.thedatum = null;
         var i = sel.indexOf(sa);
         if(i < 0)
             sel.push(sa);
@@ -1445,8 +1429,31 @@ function savePage(){
             desel.push(sa);
         }
     });
+    sel = sel.map(function(sa){
+        var c = {};
+        for(var prop in sa)
+            c[prop] = sa[prop];
+        c._prev = null;
+        c._id = null;
+        c.rank = null;
+        c.thedatum = null;
+        return c;
+    });
+    desel = desel.map(function(sa){
+        var c = {};
+        for(var prop in sa)
+            c[prop] = sa[prop];
+        c._prev = null;
+        c._id = null;
+        c.rank = null;
+        c.thedatum = null;
+        return c;
+    });
+
+    //Write page to Blob and offer it for download.
+    var loadscript_pos = PAT_LOAD_SCRIPT.exec(pagehtml);
     var b = new Blob(
-        [[pagehtml.substr(0, x.index + x[1].length),
+        [[pagehtml.substr(0, loadscript_pos.index + loadscript_pos[1].length),
         "<","script type=\"text/javascript\">",
         "var graph_spec=",JSON.stringify(graph_specx),
         ";onLoadSpec(false,true)",
@@ -1461,7 +1468,7 @@ function savePage(){
         ";document.getElementById(\"renderCanvas\").checked=",(rendererName == "canvas"? "true": "false"),
         ";parse(true);",
         "<","/script>",
-        pagehtml.substr(x.index + x[1].length + x[2].length)].join("")],
+        pagehtml.substr(loadscript_pos.index + loadscript_pos[1].length + loadscript_pos[2].length)].join("")],
         {type: "text/html"});
     if(window.navigator.msSaveOrOpenBlob)
         window.navigator.msSaveOrOpenBlob(b, fileName + ".html");

fdstools/vis/samplevis/samplevis.json

@@ -429,8 +429,12 @@
     {
       "name": "d",
       "type": "ordinal",
-      "range": ["transparent"],
-      "domain": ["\u2014 Strand balance"]
+      "range": ["black", "red"]
+    },
+    {
+      "name": "e",
+      "type": "ordinal",
+      "range": ["M-0.5,0L0.5,0", "M-0.5,0L-0.115385,0M0.115385,0L0.5,0"]
     }
   ],
   "marks": [
@@ -532,13 +536,12 @@
           }
         },
         {
-          "fill": "d",
+          "stroke": "d",
+          "shape": "e",
+          "values": ["Strand balance", "Allele threshold"],
           "properties": {
             "symbols": {
-              "stroke": {"value": "transparent"}
-            },
-            "labels": {
-              "x": {"value": 2}
+              "size": {"value": 100}
             }
           }
         }
@@ -759,6 +762,46 @@
             }
           ]
         },
+        {
+          "type": "rule",
+          "from": {
+            "transform": [
+              {
+                "type": "aggregate",
+                "groupby": ["marker"],
+                "summarize": {"xhigh": "max"}
+              },
+              {
+                "type": "lookup",
+                "on": "aggr",
+                "onKey": "marker",
+                "keys": ["marker"],
+                "as": ["aggr"],
+                "default": {"max_total_added": 0, "sum_total_added": 0}
+              },
+              {
+                "type": "formula",
+                "field": "threshold",
+                "expr": "max(allele_amplitude_threshold, allele_orientation_threshold*2, allele_amplitude_pct_threshold*datum.aggr.max_total_added/100, allele_amplitude_markerpct_threshold*datum.aggr.sum_total_added/100)"
+              },
+              {
+                "type": "filter",
+                "test": "datum.threshold <= datum.max_xhigh"
+              }
+            ]
+          },
+          "properties": {
+            "update": {
+              "x": {"scale": "x", "field": "threshold"},
+              "y": {"value": 0},
+              "y2": {"field": {"group": "height"}},
+              "stroke": {"value": "red"},
+              "strokeOpacity": {"value": 0.5},
+              "strokeWidth": {"value": 1},
+              "strokeDash": {"value": [5, 3]}
+            }
+          }
+        },
         {
           "name": "alleleSelector",
           "type": "rect",

notes.txt

@@ -4,7 +4,6 @@ To-do:
   * Detect whether correction was performed; hide related columns if not.
   * Option to choose complete table download (all columns, not all rows).
   * Option to freely adjust the sorting (currently CE length toggle only).
-  * Visualise table filtering thresholds in the graphs.
   * Some of the media query breakpoints overlap, fix this.
   * Make Samplevis more responsive when rendering/updating graphs. To do this,
     the work should be broken up into chunks and each chunk should set off the