Plotly for convergence; fixed term pair report

evoldoers · Apr 5, 2016 · 072c301 · 072c301
1 parent 7e1256a
commit 072c301
Show file tree

Hide file tree

Showing 5 changed files with 57 additions and 25 deletions.
diff --git a/Makefile b/Makefile
@@ -14,14 +14,14 @@ README.md: bin/wtfgenes.js
 	bin/wtfgenes.js -h | perl -pe 's/</&lt;/g;s/>/&gt;/g;' | perl -e 'open FILE,"<README.md";while(<FILE>){last if/<pre>/;print}close FILE;print"<pre><code>\n";while(<>){print};print"</code></pre>\n"' >temp.md
 	mv temp.md $@
 
-webclient: jquery d3 web/wtfgenes.js
+webclient: jquery plotly web/wtfgenes.js
 
 jquery: web/jquery-1.12.2.min.js
 
-d3: web/d3.v3.min.js
+plotly: web/plotly-latest.min.js
 
-web/d3.v3.min.js:
-	cd web; curl -O https://d3js.org/d3.v3.min.js
+web/plotly-latest.min.js:
+	cd web; curl -O https://cdn.plot.ly/plotly-latest.min.js
 
 web/jquery-1.12.2.min.js:
 	cd web; curl -O https://code.jquery.com/jquery-1.12.2.min.js

diff --git a/bin/wtfgenes.js b/bin/wtfgenes.js
@@ -190,7 +190,7 @@ function runInference (genesJson) {
 	mcmc.logProgress()
 
     if (logging('mixing'))
-	mcmc.analyzeMixing()
+	mcmc.logMixing()
 
     var nSamples = samplesPerTerm * mcmc.nVariables()
     if (logging('data'))

diff --git a/lib/mcmc.js b/lib/mcmc.js
@@ -55,6 +55,16 @@
 	}
     }
 
+    function logLogLikelihood() {
+	var mcmc = this
+	if (!mcmc.logLikelihoodTrace) {
+	    mcmc.logLikelihoodTrace = []
+	    mcmc.postMoveCallback.push (function (mcmc, move) {
+	            mcmc.logLikelihoodTrace.push (mcmc.quickCollapsedLogLikelihood())
+	    })
+	}
+    }
+
     function logTermPairs() {
 	var mcmc = this
 	mcmc.termPairOccupancy = mcmc.models.map (function (model) {
@@ -75,7 +85,7 @@
 	})
     }
 
-    function analyzeMixing() {
+    function logMixing() {
 	var mcmc = this
 	var startTime = Date.now(), moveStartMillisecs
 	mcmc.traceStats = { logLikelihood: [],
@@ -88,12 +98,12 @@
 	    mcmc.traceStats.nProposedMoves[type] = 0
 	})
 	mcmc.logActiveTerms()
+	mcmc.logLogLikelihood()
 	mcmc.preMoveCallback.push (function (mcmc) {
 	    moveStartMillisecs = (new Date).getTime()
 	})
 	mcmc.postMoveCallback.push (function (mcmc, move) {
 	    mcmc.traceStats.moveElapsedMillisecs[move.type] += (new Date).getTime() - moveStartMillisecs
-	    mcmc.traceStats.logLikelihood.push (mcmc.quickCollapsedLogLikelihood())
 	    ++mcmc.traceStats.nProposedMoves[move.type]
 	    if (move.accepted)
 		++mcmc.traceStats.nAcceptedMoves[move.type]
@@ -103,7 +113,7 @@
 	    summ.mcmc.samplesPerSecond = mcmc.samples / (endTime - startTime)
 	    var points = util.iota (Math.ceil(Math.log2(mcmc.samples))).map (function(x) { return Math.pow(2,x) })
 	    console.warn ("Computing log-likelihood autocorrelations")
-	    summ.mcmc.logLikeAutoCorrelation = util.autocorrelation (mcmc.traceStats.logLikelihood, points)
+	    summ.mcmc.logLikeAutoCorrelation = util.autocorrelation (mcmc.logLikelihoodTrace, points)
 	    console.warn ("Computing term autocorrelations")
 	    summ.mcmc.termAutoCorrelation = []
 	    mcmc.models.forEach (function (model, m) {
@@ -361,7 +371,8 @@
 		    logProgress: logProgress,
 		    logActiveTerms: logActiveTerms,
 		    logTermPairs: logTermPairs,
-		    analyzeMixing: analyzeMixing,
+		    logMixing: logMixing,
+		    logLogLikelihood: logLogLikelihood,
 
 		    run: run,
 		    termSummary: termSummary,

diff --git a/web/client.js b/web/client.js
@@ -57,6 +57,7 @@
 		wtf.ui.samplesPerSec.text ((wtf.samplesPerRun / elapsedSecs).toPrecision(2))
 	    }
 	    wtf.lastRun = now
+	    wtf.ui.totalSamples.text (wtf.mcmc.samples.toString())
 	    wtf.ui.samplesPerTerm.text ((wtf.mcmc.samples / wtf.mcmc.nVariables()).toString())
 	    if (wtf.redraw) {
 		var table = $('<table></table>')
@@ -67,12 +68,9 @@
 		    if (termProb[t] > interactionThreshold)
 			topTerms.push (t)
 		})
-		var termPairProb, termPairMarginal
+		var termPairProb
 		if (wtf.showPairs) {
 		    termPairProb = wtf.mcmc.termPairSummary (0, topTerms)
-		    termPairMarginal = util.keyValListToObj (topTerms.map (function(t) {
-			return [t, util.sumList (util.values (termPairProb[t]))]
-		    }))
 		}
 		table.append ($('<tr><th>Term</th><th>Probability</th>'
 				+ (wtf.showPairs
@@ -90,7 +88,7 @@
 				    + (wtf.showPairs
 				       ? (p > interactionThreshold
 					  ? topTerms.map (function(t2,i2) {
-					      var ratio = termPairProb[t][t2] / (termPairMarginal[t] * termPairMarginal[t2])
+					      var ratio = termPairProb[t][t2] / (termProb[t] * termProb[t2])
 					      var rStyle = i==i2 ? blankStyle() : ratioStyle(ratio)
 					      return '<td ' + rStyle + '>' + (i == i2 ? '' : ratioText(ratio) + '</td>')
 					  }).join('')
@@ -107,6 +105,22 @@
         }
     }
 
+    function plotLogLikelihood() {
+        var wtf = this
+        Plotly.plot( wtf.ui.logLikePlot[0], [{
+	    y: wtf.mcmc.logLikelihoodTrace }],
+                     { title: "Convergence",
+                       xaxis: { title: "Number of samples" },
+                       yaxis: { title: "Log-likelihood" } } )
+        setTimeout (redrawLogLikelihood.bind(wtf), 100)
+    }
+
+    function redrawLogLikelihood() {
+        var wtf = this
+        Plotly.redraw( wtf.ui.logLikePlot[0] )
+        setTimeout (redrawLogLikelihood.bind(wtf), 100)
+    }
+
     function cancelStart(wtf,msg) {
 	alert (msg)
         wtf.ui.startButton.prop('disabled',false)
@@ -148,24 +162,30 @@
 				   seed: 123456789
 			         })
 
+            wtf.mcmc.logLogLikelihood()
+
             resumeAnalysis.call(wtf)
             wtf.ui.startButton.prop('disabled',false)
 
-	    wtf.ui.interButton = $('<button>Track pairs</button>')
+	    wtf.ui.interButton = $('<button>Track co-occurence</button>')
 	    wtf.ui.interButton.click (function() {
 		wtf.ui.interButton.prop('disabled',true)
 		wtf.mcmc.logTermPairs()
 		wtf.showPairs = true
+                if (wtf.paused)
+                    resumeAnalysis.call(wtf)
 	    })
 
+	    wtf.ui.totalSamples = $('<span>0</span>')
 	    wtf.ui.samplesPerTerm = $('<span>0</span>')
 	    wtf.ui.samplesPerSec = $('<span>0</span>')
 	    wtf.ui.mcmcStats = $('<span/>')
-	    wtf.ui.mcmcStats.append (" ", wtf.ui.samplesPerTerm, " samples/term, ", wtf.ui.samplesPerSec, " samples/sec")
+	    wtf.ui.mcmcStats.append (" ", wtf.ui.totalSamples, " samples (", wtf.ui.samplesPerTerm, " samples/term, ", wtf.ui.samplesPerSec, " samples/sec)")
 
 	    wtf.ui.inputDiv.append (wtf.ui.interButton, wtf.ui.mcmcStats)
-
+            
             runMCMC.call(wtf)
+            plotLogLikelihood.call(wtf)
         }
     }
 
@@ -267,8 +287,9 @@
                                     wtf.ui.startButton)
 
             wtf.ui.resultsDiv = $('<div/>')
+	    wtf.ui.logLikePlot = $('<div/>')
 	    wtf.ui.tableParent = $('<div/>')
-	    wtf.ui.resultsDiv.append (wtf.ui.tableParent)
+	    wtf.ui.resultsDiv.append (wtf.ui.logLikePlot, wtf.ui.tableParent)
 
             wtf.ui.parentDiv.append (wtf.ui.inputDiv,
 				     '<br/>',

diff --git a/web/index.html b/web/index.html
@@ -1,16 +1,12 @@
 <html>
   <head>
-<title>WTF genes?!?</title>
-</head>
-<body>
-<h1>WTF genes?!?</h1>
-<b>W</b>hat is <b>T</b>he <b>F</b>unction of these <b>genes</b>?
+<title>WTF genes?</title>
 
     <!-- JQuery -->
     <script type="text/javascript" src="jquery-1.12.2.min.js"></script>
 
-    <!-- d3 -->
-    <script type="text/javascript" src="d3.v3.min.js"></script>
+    <!-- Plotly -->
+    <script type="text/javascript" src="plotly-latest.min.js"></script>
 
     <!-- WTFgenes -->
     <script type="text/javascript" src="wtfgenes.js"></script>
@@ -23,5 +19,9 @@ <h1>WTF genes?!?</h1>
       })
     </script>
 
+  </head>
+<body>
+<h1>WTF genes?</h1>
+<b>W</b>hat is <b>T</b>he <b>F</b>unction of these <b>genes</b>?
 </body>
 </html>