Add Samplevis option to apply graph filtering before noise correction

README.rst

@@ -29,6 +29,9 @@ Alternatively, FDSTools can be installed by running:
 
 FDSTools Changelog
 ------------------
+v1.1.2
+    - Includes Samplevis v2.2.1
+
 v1.1.1
     - Includes TSSV v1.1.1
 
@@ -616,6 +619,10 @@ v1.0.0
 
 Samplevis
 ~~~~~~~~~
+v2.2.1
+    - Added an option to apply graph filtering before noise correction (on by
+      default)
+
 v2.2.0
     - Fixed incorrect calculation of 'percentage of highest' if the 'sequence'
       with the highest read count within a marker is the aggregated 'Other

fdstools/vis/samplevis/index.html

@@ -24,7 +24,7 @@
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width, initial-scale=1">
     <title>Sample Visualisation - FDSTools</title>
-    <!-- VERSION 2.1.2 -->
+    <!-- VERSION 2.2.1 -->
     <!-- BEGIN_LIBRARIES -->
     <script src="https://vega.github.io/vega-editor/vendor/d3.min.js"></script>
     <script src="https://vega.github.io/vega/vega.min.js"></script>
@@ -531,6 +531,14 @@
                         </label>
                     </td>
                 </tr>
+                <tr>
+                    <td colspan="2">
+                        <label>
+                            <input type="checkbox" id="filteruncorrected" checked>
+                            Filter before noise correction
+                        </label>
+                    </td>
+                </tr>
                 <tr>
                     <td colspan="2">
                         <label>
@@ -1667,6 +1675,9 @@ function onLoadSpec(has_data, no_file_chooser){
     document.getElementById("shownegative").addEventListener('change', function(){
         setSignalValue("show_negative", this.checked);
     }, false);
+    document.getElementById("filteruncorrected").addEventListener('change', function(){
+        setSignalValue("filter_uncorrected", this.checked);
+    }, false);
     document.getElementById("showother").addEventListener('change', function(){
         setSignalValue("show_other", this.checked);
     }, false);
@@ -1701,6 +1712,7 @@ function onLoadSpec(has_data, no_file_chooser){
     document.getElementById("minOa").value = getSignalValue("allele_orientation_threshold");
     document.getElementById("minBias").value = getSignalValue("bias_threshold");
     document.getElementById("shownegative").checked = getSignalValue("show_negative");
+    document.getElementById("filteruncorrected").checked = getSignalValue("filter_uncorrected");
     document.getElementById("showother").checked = getSignalValue("show_other");
     document.getElementById("sortstrbylength").checked = getSignalValue("sort_str_by_length");
     document.getElementById("commonrange").checked = (graph_spec.marks[1].scales[0].domain.data == "table");

fdstools/vis/samplevis/samplevis.json

 {
-  "fdstools_visversion": "2.2.0",
+  "fdstools_visversion": "2.2.1",
   "width": 600,
   "height": 10,
   "signals": [
@@ -47,6 +47,10 @@
       "name": "show_negative",
       "init": true
     },
+    {
+      "name": "filter_uncorrected",
+      "init": true
+    },
     {
       "name": "show_other",
       "init": true
@@ -181,7 +185,7 @@
         {
           "type": "aggregate",
           "groupby": ["marker"],
-          "summarize": {"total_added": ["max"]}
+          "summarize": {"total_added": ["max"], "total": ["max"]}
         }
       ]
     },
@@ -196,7 +200,7 @@
         {
           "type": "aggregate",
           "groupby": ["marker"],
-          "summarize": {"total_added": ["sum"]}
+          "summarize": {"total_added": ["sum"], "total": ["sum"]}
         }
       ]
     },
@@ -230,6 +234,16 @@
           "field": "pct_of_sum",
           "expr": "datum.aggrs.sum_total_added? (datum.total_added / datum.aggrs.sum_total_added * 100) : 100"
         },
+        {
+          "type": "formula",
+          "field": "pct_of_max_uncorrected",
+          "expr": "datum.aggrm.max_total? (datum.total / datum.aggrm.max_total * 100) : 100"
+        },
+        {
+          "type": "formula",
+          "field": "pct_of_sum_uncorrected",
+          "expr": "datum.aggrs.sum_total? (datum.total / datum.aggrs.sum_total * 100) : 100"
+        },
         {
           "type": "formula",
           "field": "strlength",
@@ -316,7 +330,7 @@
         {
           "type": "formula",
           "field": "sequence",
-          "expr": "((show_negative? abs(datum.total_added) : datum.total_added) >= amplitude_threshold && (show_negative? abs(datum.pct_of_max) : datum.pct_of_max) >= amplitude_pct_threshold && (show_negative? abs(datum.pct_of_sum) : datum.pct_of_sum) >= amplitude_markerpct_threshold && min(show_negative? abs(datum.forward_added) : datum.forward_added, show_negative? abs(datum.reverse_added) : datum.reverse_added) >= orientation_threshold)? datum.sequence : 'Other sequences'"
+          "expr": "((show_negative? abs(filter_uncorrected? datum.total : datum.total_added) : filter_uncorrected? datum.total : datum.total_added) >= amplitude_threshold && (show_negative? abs(filter_uncorrected? datum.pct_of_max_uncorrected : datum.pct_of_max) : filter_uncorrected? datum.pct_of_max_uncorrected : datum.pct_of_max) >= amplitude_pct_threshold && (show_negative? abs(filter_uncorrected? datum.pct_of_sum_uncorrected : datum.pct_of_sum) : filter_uncorrected? datum.pct_of_sum_uncorrected : datum.pct_of_sum) >= amplitude_markerpct_threshold && min(show_negative? abs(filter_uncorrected? datum.forward : datum.forward_added) : filter_uncorrected? datum.forward : datum.forward_added, show_negative? abs(filter_uncorrected? datum.reverse : datum.reverse_added) : filter_uncorrected? datum.reverse : datum.reverse_added) >= orientation_threshold)? datum.sequence : 'Other sequences'"
         },
         {
           "type": "filter",