Merge pull request #55 from bd2kccd/v1.3.3

V1.3.3
bd2kccd · Apr 7, 2017 · bb948ac · bb948ac
2 parents 5faa71d + c4f76d9
commit bb948ac
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Showing 13 changed files with 83 additions and 25 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-web</artifactId>
-    <version>1.4.0</version>
+    <version>1.3.3</version>
     <packaging>jar</packaging>
 
     <name>causal-web</name>

diff --git a/src/main/resources/ccd.properties b/src/main/resources/ccd.properties
@@ -44,7 +44,7 @@ ccd.email.admin.sendto=${spring.mail.username}
 ccd.acct.reg.activ.required=false
 
 # LABELS
-ccd.app.title=Causal Web v1.3.2
+ccd.app.title=Causal Web v1.3.3
 ccd.app.copyright=University of Pittsburgh and Carnegie Mellon University
 
 ccd.app.agreement=TERMS AND CONDITIONS&#10;&#10;\

diff --git a/src/main/resources/static/img/pags/ab_bidirect.png b/src/main/resources/static/img/pags/ab_bidirect.png
diff --git a/src/main/resources/static/img/pags/ab_direct.png b/src/main/resources/static/img/pags/ab_direct.png
diff --git a/src/main/resources/static/img/pags/ab_pd_bidirect.png b/src/main/resources/static/img/pags/ab_pd_bidirect.png
diff --git a/src/main/resources/static/img/pags/ab_pd_direct.png b/src/main/resources/static/img/pags/ab_pd_direct.png
diff --git a/src/main/resources/static/img/pags/small_ab_bidirect.png b/src/main/resources/static/img/pags/small_ab_bidirect.png
diff --git a/src/main/resources/static/img/pags/small_ab_direct.png b/src/main/resources/static/img/pags/small_ab_direct.png
diff --git a/src/main/resources/static/img/pags/small_ab_pd_bidrect.png b/src/main/resources/static/img/pags/small_ab_pd_bidrect.png
diff --git a/src/main/resources/static/img/pags/small_ab_pd_direct.png b/src/main/resources/static/img/pags/small_ab_pd_direct.png
diff --git a/src/main/resources/static/js/algo/d3jsplot.js b/src/main/resources/static/js/algo/d3jsplot.js
@@ -70,13 +70,12 @@ function plotGraph(links) {
 
     // Default distance accessor is 30
     simulation.force("link")
-            .distance(60);
+            .distance(50);
 
     // Each node conects to itself, so we can highlight this node when it's selected
     for (i = 0; i < nodes.length; i++) {
         linkedByIndex[i + "," + i] = 1;
     }
-    ;
 
     // Add all the connections based on links
     // Must call this after  simulation.force("link").links(links)
@@ -208,29 +207,25 @@ function plotGraph(links) {
     function ticked() {
         // Position nodes
         node.attr("cx", function (d) {
-            // This makes sure the nodes won't go out of the container
-            // Bounding box example: http://mbostock.github.io/d3/talk/20110921/bounding.html
-            return d.x = Math.max(nodeRadius, Math.min(svgWidth - nodeRadius, d.x));
-            //return d.x;
-        })
-                .attr("cy", function (d) {
-                    return d.y = Math.max(nodeRadius, Math.min(svgHeight - nodeRadius, d.y));
-                    //return d.y;
-                });
+                return d.x;
+            })
+            .attr("cy", function (d) {
+                return d.y;
+            });
 
         // Position links
         // Use path instead of line since IE 10 doesn't render the links correctly
         link.attr("d", positionLink).each(function () {
-            this.parentNode.insertBefore(this, this);
-        });
+                this.parentNode.insertBefore(this, this);
+            });
 
         // Position node text
         text.attr("x", function (d) {
-            return d.x + nodeRadius;
-        })
-                .attr("y", function (d) {
-                    return d.y + nodeRadius / 2;
-                });
+                return d.x - (nodeRadius / 2);
+            })
+            .attr("y", function (d) {
+                return d.y - (1.5 * nodeRadius);
+            });
     }
 
     // Position the edge link

diff --git a/src/main/resources/static/js/algo/d3jsplot.min.js b/src/main/resources/static/js/algo/d3jsplot.min.js
diff --git a/src/main/resources/templates/algorithm/plot.html b/src/main/resources/templates/algorithm/plot.html
@@ -34,13 +34,75 @@
                     <div class="col-lg-12">
                         <h3 class="page-header">Causal Graph of <span class="label label-primary" th:text="${plot}">Title</span></h3>
                         <ul>
-                        <li>You can use the mouse wheel to zoom in/out this graph.</li>
-                        <li>You can drag the entire graph by dragging an empty space on the graph.</li>
-                        <li>You can highlight a node and all the edges of this node by double clicking the node, and double clicking again on any node to disable the highlighting.</li>
-                        <li>You can search and locate a node by entering its name(case-insensitive) in the search box.</li>
+                            <li>You can use the mouse wheel to zoom in/out this graph.</li>
+                            <li>You can drag the entire graph by dragging an empty space on the graph.</li>
+                            <li>You can highlight a node and all the edges of this node by double clicking the node, and double clicking again on any node to disable the highlighting.</li>
+                            <li>You can search and locate a node by entering its name(case-insensitive) in the search box.</li>
                         </ul>
                     </div>
                 </div>
+                <div class="row">
+                    <div class="col-lg-12">
+                        <div class="panel panel-primary">
+                            <div class="panel-body">
+                                <table class="table table-responsive">
+                                    <thead>
+                                        <tr>
+                                            <th>Edge Types</th>
+                                            <th>Present Relationships</th>
+                                            <th>Absent Relationships</th>
+                                        </tr>
+                                    </thead>
+                                    <tbody>
+                                        <tr>
+                                            <td><img src="../../static/img/pags/small_ab_direct.png" th:src="@{/img/pags/small_ab_direct.png}" alt="A --&gt; B" /></td>
+                                            <td>
+                                                A is a cause of B.<br />
+                                                It may be a direct or indirect cause that may include other measured variables. Also, there may be an unmeasured confounder of A and B.
+                                            </td>
+                                            <td>B is not a cause of A</td>
+                                        </tr>
+                                        <tr>
+                                            <td><img src="../../static/img/pags/small_ab_bidirect.png" th:src="@{/img/pags/small_ab_bidirect.png}" alt="A &lt;-&gt; B" /></td>
+                                            <td>There is an unmeasured confounder (call it L) of A and B. There may be measured variables along the causal pathway from L to A or from L to B.</td>
+                                            <td>
+                                                A is not a cause of B.<br />
+                                                B is not a cause of A.
+                                            </td>
+                                        </tr>
+                                        <tr>
+                                            <td><img src="../../static/img/pags/small_ab_pd_direct.png" th:src="@{/img/pags/small_ab_pd_direct.png}" alt="A o-&gt; B" /></td>
+                                            <td>Either A is a cause of B (i.e, A --&gt; B) or there is an unmeasured confounder of A and B (i.e, A &lt;-&gt; B) or both.</td>
+                                            <td>B is not a cause of A.</td>
+                                        </tr>
+                                        <tr>
+                                            <td><img src="../../static/img/pags/small_ab_pd_bidrect.png" th:src="@{/img/pags/small_ab_pd_bidrect.png}" alt="A o-o B" /></td>
+                                            <td>
+                                                Exactly one of the following holds:
+                                                <ol>
+                                                    <li>A is a cause of B</li>
+                                                    <li>B is a cause of A</li>
+                                                    <li>there is an unmeasured confounder of A and B</li>
+                                                    <li>both a and c</li>
+                                                    <li>both b and c</li>
+                                                </ol>
+                                            </td>
+                                            <td></td>
+                                        </tr>
+                                    </tbody>
+                                    <tfoot>
+                                        <tr>
+                                            <td colspan="3">If an edge is dashed that means there is no latent confounder. Otherwise, there is possibly latent confounder.</td>
+                                        </tr>
+                                        <tr>
+                                            <td colspan="3">If an edge is green that means it is definitely direct. Otherwise, it is possibly direct.</td>
+                                        </tr>
+                                    </tfoot>
+                                </table>
+                            </div>
+                        </div>
+                    </div>
+                </div>
                 <div class="row">
                     <div class="col-lg-12">
                         <iframe src="#" th:src="@{/algorithm/results/d3graph(file=${fileName})}" marginwidth="0" marginheight="0" scrolling="no"></iframe>