Resove #29: enrichment tool tweaks

- BP is default - Add links to gene symbols - Reorganize elements - Add a genes backing top terms section - Clicking similarity chart now changes table data - Fix tooltips and dialog sigfigs in stab. chart - Add more contextual help to stability chart - Easier to see when buttons are selected
PavlidisLab · Mar 22, 2018 · 52af450 · 52af450
1 parent 6d807f1
commit 52af450
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Showing 9 changed files with 147 additions and 190 deletions.
diff --git a/gotrack/src/main/java/ubc/pavlab/gotrack/analysis/EnrichmentAnalysisOptions.java b/gotrack/src/main/java/ubc/pavlab/gotrack/analysis/EnrichmentAnalysisOptions.java
@@ -20,5 +20,5 @@ public class EnrichmentAnalysisOptions {
     private int maxAnnotatedPopulation = 200; // maximum geneset size a specific term must have to be included in results
     private MultipleTestCorrection multipleTestCorrection = MultipleTestCorrection.BH; // method of multiple tests correction
     private double threshold = 0.05; // tEither p-value cutoff if using Bonferroni or FDR level if using BH step-up
-    private List<Aspect> aspects = Lists.newArrayList( Aspect.values() ); // Aspect restriction
+    private List<Aspect> aspects = Lists.newArrayList( Aspect.BP ); // Aspect restriction
 }
diff --git a/gotrack/src/main/java/ubc/pavlab/gotrack/analysis/SimilarityAnalysis.java b/gotrack/src/main/java/ubc/pavlab/gotrack/analysis/SimilarityAnalysis.java
@@ -19,25 +19,17 @@
 
 package ubc.pavlab.gotrack.analysis;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
 import com.google.common.collect.Iterables;
-
+import org.apache.log4j.Logger;
 import ubc.pavlab.gotrack.beans.Cache;
 import ubc.pavlab.gotrack.model.Edition;
 import ubc.pavlab.gotrack.model.Gene;
 import ubc.pavlab.gotrack.model.go.GeneOntologyTerm;
 import ubc.pavlab.gotrack.utilities.Jaccard;
 import ubc.pavlab.gotrack.utilities.Tversky;
 
+import java.util.*;
+
 /**
  * Calculates scores which attempt to explore the impact that annotation similarity has on the performance of
  * gene set enrichment analyses. The methods of exploration for similarity compare previous annotations for each gene
@@ -185,7 +177,7 @@ public Map<Edition, SimilarityScore> getSimilarityScores() {
         return similarityScores;
     }
 
-    public SimilarityScore getSimilarityScores( Edition ed ) {
+    public SimilarityScore getSimilarityScore( Edition ed ) {
         if ( ed == null ) return null;
         return similarityScores.get( ed );
     }

diff --git a/gotrack/src/main/java/ubc/pavlab/gotrack/beans/EnrichmentView.java b/gotrack/src/main/java/ubc/pavlab/gotrack/beans/EnrichmentView.java
@@ -736,15 +736,6 @@ private Map<Edition, Map<GeneOntologyTerm, EnrichmentResult>> filter( Set<GeneOn
 
     }
 
-    /**
-     * Entry point for retrieving data on click of similarity chart
-     */
-    public void fetchSimilarityInformation() {
-        Integer edition = Integer.valueOf(
-                FacesContext.getCurrentInstance().getExternalContext().getRequestParameterMap().get( "edition" ) );
-        Edition ed = cache.getEdition( selectedSpecies, edition );
-        selectedSimilarityScore = combinedAnalysis.getSimilarityAnalysis().getSimilarityScores( ed );
-    }
 
     /**
      * Used for clicks on data points in enrichment/stability chart
@@ -792,15 +783,20 @@ private void resetFetchTermInformation() {
         selectedValueName = null;
     }
 
-    // Enrichment Table ---------------------------------------------------------------------------------------
 
-    public void loadEnrichmentTableData() {
+    /**
+     * Used for clicks on data points in term/similarity charts
+     */
+    public void loadTableData() {
         Integer edition = Integer.valueOf(
                 FacesContext.getCurrentInstance().getExternalContext().getRequestParameterMap().get( "edition" ) );
         Edition ed = cache.getEdition( selectedSpecies, edition );
         loadEnrichmentTableData( ed );
+        selectedSimilarityScore = combinedAnalysis.getSimilarityAnalysis().getSimilarityScore( ed );
     }
 
+    // Enrichment Table ---------------------------------------------------------------------------------------
+
     /**
      * Prepares data for enrichment table
      */

diff --git a/gotrack/src/main/webapp/enrichment.xhtml b/gotrack/src/main/webapp/enrichment.xhtml
diff --git a/gotrack/src/main/webapp/resources/composites/enrichmentResultsTable.xhtml b/gotrack/src/main/webapp/resources/composites/enrichmentResultsTable.xhtml
@@ -22,12 +22,12 @@
 <composite:implementation>
     <p:dataTable id="enrichmentTable" widgetVar="tableEnrichmentWdg"
                  var="entry" value="#{cc.attrs.value}"
-                 sortMode="multiple" style="margin-bottom:0"
+                 sortMode="multiple" style="margin-bottom:0;max-height: 225px;"
                  emptyMessage="No enrichment data found for selected edition"
                  filteredValue="#{cc.attrs.filteredValue}"
                  rowStyleClass="#{entry.significant == true ? 'significant' : 'not-significant'}"
                  styleClass="ui-table-exporter-align-right ui-table-graph-float-left"
-                 scrollable="true" scrollHeight="300"
+                 scrollable="true"
                  selectionMode="multiple"
                  selection="#{cc.attrs.selection}"
                  rowKey="#{entry.term.goId}"
@@ -37,23 +37,6 @@
         <p:ajax event="filter"
                 oncomplete="postAjaxSortTable(PF('tableEnrichmentWdg'))"/>
 
-        <f:facet name="header">
-            <p:overlayPanel for="tableHelpBtn" hideEffect="fade" appendToBody="true">
-                <div class="overlay-help">
-                    <p>This table shows enrichment data for those terms that were significantly enriched in this edition as well as those that were significant at some point in their history.</p>
-                    <p>
-                        This means that not every term in the table is significant at the currently chosen edition, but it was necessarily significant as some point.
-                    </p>
-                </div>
-            </p:overlayPanel>
-            <p:commandButton  id="tableHelpBtn" value=""
-                              styleClass="no-value no-background fa-fix noupdate"
-                              icon="fa fa-question-circle" type="button"
-                              style="vertical-align: text-top;float: left;"/>
-            <p:outputPanel id="headerPanel" rendered="#{cc.attrs.header != null}">
-                <h:outputText value="#{cc.attrs.header}"/>
-            </p:outputPanel>
-        </f:facet>
 
         <f:facet name="footer">
             <!-- &#8203 is a zero-width space so that the div container leaves space for the status text -->

diff --git a/gotrack/src/main/webapp/resources/composites/geneTable.xhtml b/gotrack/src/main/webapp/resources/composites/geneTable.xhtml
@@ -17,7 +17,7 @@
 
 <composite:implementation>
 
-    <p:dataTable var="gene" value="#{cc.attrs.value}" emptyMessage="No genes found." style="width:100%;" scrollable="true">
+    <p:dataTable var="gene" value="#{cc.attrs.value}" emptyMessage="No genes found." style="width:100%;max-height: 200px;" scrollable="true" scrollRows="25">
         <p:column headerText="Symbol" style="width:120px;">
             <a href="http://www.uniprot.org/uniprot/#{gene.accession.accession}"
                target="_blank" style="margin-right: 5px; text-decoration: none;">

diff --git a/gotrack/src/main/webapp/resources/css/common.css b/gotrack/src/main/webapp/resources/css/common.css
@@ -288,4 +288,11 @@ div.inline {
 .ui-rowgroup-header.ui-datatable-headerrow.ui-widget-header > td {
     padding-top: 10px;
     padding-bottom: 10px;
+}
+/* Easier to see when button is selected */
+div.ui-selectmanybutton > div.ui-button.ui-widget.ui-state-default.ui-button-text-only {
+    color: rgba(0, 0, 0, 0.4);
+}
+div.ui-selectmanybutton > div.ui-button.ui-widget.ui-state-default.ui-button-text-only.ui-state-active {
+    color: inherit;
 }
diff --git a/gotrack/src/main/webapp/resources/css/enrichment.css b/gotrack/src/main/webapp/resources/css/enrichment.css
@@ -15,12 +15,12 @@ table.no-border, table.no-border tr, table.no-border td {
     line-height: 16px;
 }
 
-#left li.ui-datalist-item > span {
+#left li.ui-datalist-item > span, #left li.ui-datalist-item > a {
     display: inline-block;
     vertical-align: middle;
 }
 
-#left li.ui-datalist-item > a {
+#left li.ui-datalist-item > a.ui-icon {
     display: inline-block;
     vertical-align: sub;
     margin-right: 10px;

diff --git a/gotrack/src/main/webapp/resources/js/enrichment.js b/gotrack/src/main/webapp/resources/js/enrichment.js
@@ -149,12 +149,6 @@ function createTermsChart(xhr, status, args) {
     var options = plotting.defaultHCOptions('hc_terms_container', args.HC_terms.chart);
     commonOptions(options, args.HC);
 
-    options.xAxis.crosshair = {
-        width: 1,
-        color: 'red',
-        dashStyle: 'shortdot'
-    };
-
     options.subtitle = {
         text: "<b>&lt;Click&gt;</b> to view enrichment results at a specific date.",
         style: {"font-size": "10px"}
@@ -180,20 +174,6 @@ function createSimilarityChart(xhr, status, args) {
 
     // options.yAxis.minorTickInterval = 0.05;
 
-    options.chart.events = {
-        click: function (event) {
-            fetchSimilarityInformation([{name: 'edition', value: GLOBALS.dateToEdition[this.hoverPoint.x]}]);
-        }
-    };
-
-    options.plotOptions.series.point = {
-        events: {
-            click: function () {
-                fetchSimilarityInformation([{name: 'edition', value: GLOBALS.dateToEdition[this.x]}]);
-            }
-        }
-    };
-
     options.tooltip.pointFormatter = function () {
         return '<span style="color:' + this.color + '">\u25CF</span> ' + this.series.name + ': <b>' + utility.sigFigs(this.y, 2) + '</b><br/>';
     }
@@ -255,6 +235,12 @@ function commonOptions(options, config) {
             clickBehaviour(event, p);
         }
     };
+
+    options.xAxis.crosshair = {
+        width: 1,
+        color: 'red',
+        dashStyle: 'shortdot'
+    };
 }
 
 function handleGraphSelected(xhr, status, args) {
@@ -584,7 +570,15 @@ function handleGraphSelected(xhr, status, args) {
         // We bypass this via a string type adaptor for Infinity and NaN
         for (var key in dateToStabilityScore) {
             if (dateToStabilityScore.hasOwnProperty(key)) {
-                dateToStabilityScore[key] = Number(dateToStabilityScore[key]);
+                var stabilityScore = dateToStabilityScore[key];
+                if (stabilityScore === 'Infinity') {
+                    stabilityScore = 'No Change';
+                } else if (stabilityScore === 'NaN') {
+                    stabilityScore = 'No Data';
+                } else {
+                    stabilityScore = utility.sigFigs(stabilityScore, 3)
+                }
+                dateToStabilityScore[key] = stabilityScore;
             }
         }
 
@@ -598,7 +592,7 @@ function handleGraphSelected(xhr, status, args) {
                     '</p><p>Date: ' + new Date(this.x).toLocaleDateString() +
                     "</p><p>Edition: " + GLOBALS.dateToEdition[this.x] +
                     "</p><p>P-value: " + utility.sigFigs(this.y, 3) +
-                    "</p><p>Stability Score: " + utility.sigFigs(dateToStabilityScore[this.x], 3) +
+                    "</p><p>Stability Score: " + dateToStabilityScore[this.x] +
                     "</p>";
             }
         }