From: miles <miles@localhost>
Date: Fri, 15 Mar 2013 22:42:37 +0000 (+0000)
Subject: not sure if heatmap is working, wanted something to revert to
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=5ff50343131b2a4a099a5bbbb061e4c4cc6454a4;p=old-jaiswallab-svn%2F.git

not sure if heatmap is working, wanted something to revert to

svn path=/; revision=436
---

diff --git a/Personnel/miles/Web Page/heatMap.php b/Personnel/miles/Web Page/heatMap.php
index c4e4154..ad0f06c 100644
--- a/Personnel/miles/Web Page/heatMap.php	
+++ b/Personnel/miles/Web Page/heatMap.php	
@@ -222,7 +222,7 @@ function drawMap(init) {
   scrolledTop = document.getElementById("scrollDiv").scrollTop - topScrollOffset +25; // NOTE the 25 accounts for the scrollbar offset allowing for scrolling up/left
   if(scrolledLeft > speciesCount*cellSize - maxCols*cellSize) {
     scrolledLeft = speciesCount*cellSize - maxCols*cellSize;
-  }
+  } //TODO examine this ^
   if(scrolledLeft < 0) {
     scrolledLeft = 0;
   }
diff --git a/Personnel/miles/Web Page/infoChoice.php b/Personnel/miles/Web Page/infoChoice.php
index 0d0a694..5d87ce4 100644
--- a/Personnel/miles/Web Page/infoChoice.php	
+++ b/Personnel/miles/Web Page/infoChoice.php	
@@ -125,13 +125,22 @@ mysql_close($connection);
       echo "<br> <br>\n";
 
       $genes="";
+      $first=true;
       $row = mysql_fetch_row($results);
       while($row != null) {
+
+	
 	echo "<a href=\"http://planteome.cgrb.oregonstate.edu/node/11?species=" . $species . "&gene=" . $row[0] . "\">" . $row[0] . "</a> <br>";
-	$genes = $genes . $row[0] . ",";
+	if($first) {
+	  $first = false;
+	  $genes = $genes . $row[0];
+	} else {
+	  $genes = $genes . "," . $row[0];
+	}
 	$row = mysql_fetch_row($results);
 	}
       mysql_close($connection);
+      echo $genes;
 }
 
 ?>
diff --git a/Personnel/miles/Web Page/viewOntology.php b/Personnel/miles/Web Page/viewOntology.php
index 1a8e4b6..cb2f557 100644
--- a/Personnel/miles/Web Page/viewOntology.php	
+++ b/Personnel/miles/Web Page/viewOntology.php	
@@ -25,15 +25,14 @@ $connection=mysql_connect($url,$username,$password);
 mysql_select_db($database);
 
 $logic = "where full_name like '";
-for($i = 0; $i + 1 < sizeof($genes); $i ++) { // note that the last parameter of $genes is an empty array
+for($i = 0; $i < sizeof($genes); $i ++) { // note that the last parameter of $genes is an empty array
   $toAdd = $genes[$i] . "'";
-  if($i + 2 < sizeof($genes)) {
+  if($i + 1 < sizeof($genes)) {
     $toAdd = $toAdd . " or full_name like '";
   }
   $logic = $logic . $toAdd;
   
 }
-echo "<br> logic: " . $logic . "<br>";
 $query="select id from gene_product " . $logic . " order by id";
 $results=mysql_query($query);
 
@@ -43,11 +42,10 @@ for($row = mysql_fetch_row($results); $row != null; $row = mysql_fetch_row($resu
   $geneProductIDs[$i] = $row[0];
   $i++;
   }
-
 $logic = "where gene_product_id=";
-for($i = 0; $i + 1 < sizeof($geneProductIDs); $i++) {
+for($i = 0; $i < sizeof($geneProductIDs); $i++) {
   $toAdd = $geneProductIDs[$i];
-  if($i + 2 < sizeof($geneProductIDs)) {
+  if($i + 1 < sizeof($geneProductIDs)) {
     $toAdd = $toAdd . " or gene_product_id=";
   }
   $logic = $logic . $toAdd;
@@ -63,9 +61,9 @@ for($row = mysql_fetch_row($results); $row != null; $row = mysql_fetch_row($resu
   }
 
 $logic = "where id='";
-for($i = 0; $i + 1 < sizeof($termIDs); $i++) {
+for($i = 0; $i < sizeof($termIDs); $i++) {
   $toAdd = $termIDs[$i] . "'";
-  if($i + 2 < sizeof($termIDs)) {
+  if($i + 1 < sizeof($termIDs)) {
     $toAdd = $toAdd . " or id='";
   }
   $logic = $logic . $toAdd;
@@ -80,6 +78,47 @@ for($row = mysql_fetch_row($results); $row != null; $row = mysql_fetch_row($resu
   $i++;
   }
 
+
+$cellData;
+//TODO this part needs the most optimization. It's really bad.
+//theoretically this should return a two-dimensional array of booleans, representing whether or not each gene is referenced to each term
+for($i = 0; $i < sizeof($genes); $i++) {
+  $query="select id from gene_product where full_name='" . $genes[$i] . "'";
+  $results=mysql_query($query);
+  $row = mysql_fetch_row($results);
+  $productID = $row[0];
+
+  $query="select term_id from association where gene_product_id='" . $productID . "'";
+  $results=mysql_query($query);
+
+  $k = 0;
+  $geneTerms;
+  for($row = mysql_fetch_row($results); $row != null; $row = mysql_fetch_row($results)) {
+    $geneTerms[$k] = $row[0];
+    $k++;
+  }
+  for($j=0;$j<sizeof($termIDs);$j++) {
+    $cellData[$i][$j] = 0;
+  }
+  for($j = 0; $j < sizeof($geneTerms);$j++) {
+    for($m = 0; $m<sizeof($termIDs);$m++) {
+      if($geneTerms[$j]==$termIDs[$m]) {
+	$cellData[$i][$m] = 1;
+      }
+    }
+  }
+}
+
+$finalCellData;
+for ($i = 0; $i < sizeof($cellData); $i ++)
+  {
+  $finalCellData[$i] = implode(",", $cellData[$i]);
+  }
+
+
+
+
+
 ?>
 
 <div id="canvasDiv" style="overflow: hidden; float: left; height: 500px; width: 1100px;">
@@ -88,11 +127,19 @@ Your browser does not support the canvas element.
 </canvas> </div>
 
 <div id="scrollDiv" style="overflow: auto; float: left; height: 515px; width: 15px;" onscroll="drawMap();">
-<canvas id="nothing" width="1" height="<?php echo 250 + sizeof($allClusterIDs)*25 ?>"> </canvas>
+<canvas id="nothing" width="1" height="<?php echo 250 + sizeof($genes)*25 ?>"> </canvas>
 </div>
 
 
 <script type="text/javascript">
+
+var rawCellData = "<?php echo implode(";",$finalCellData); ?>";
+var rareCellData = rawCellData.split(";");
+var cellData = new Array(rareCellData.length);
+for(var i=0; i<rareCellData.length; i++) {
+  cellData[i] = rareCellData[i].split(",");
+  }
+
 var rawGenes = "<?php echo $_POST['param'] ?>";
 var genes = rawGenes.split(",");
 var geneCount = genes.length;
@@ -106,12 +153,14 @@ var ontMap = canvas.getContext("2d");
 var startTerm = 0;
 
 var topOffset = 210;
-var leftOffset = 50;
+var leftOffset = 85;
 
-var cellSize = 10;
+var cellSize = 15;
 var maxRows = Math.floor((500-topOffset)/cellSize);
 var maxCols = Math.floor((1000-leftOffset)/cellSize);
 
+var borderWidth = 1;
+
 
 function drawTerms(startTerm) {
   //black for text
@@ -135,11 +184,90 @@ function drawTerms(startTerm) {
   ontMap.translate(topOffset,0);
   ontMap.rotate(90*Math.PI/180);
 }
+
+function drawGenes(startGene) {
+  ontMap.fillStyle = "#000000";
+  for(var c=startGene; (c<geneCount) && (c<=startGene + maxRows); c++) {
+    ontMap.fillText(genes[c],5,(c-startGene)*cellSize + topOffset + cellSize/2);
+  }
+}
+drawGenes(0);
 drawTerms(0);
 
+function drawMap(init) {
+  scrolledLeft = document.getElementById("scrollDiv").scrollLeft;
+  scrolledTop = document.getElementById("scrollDiv").scrollTop;
+  if(scrolledLeft > termCount*cellSize - maxCols*cellSize) {
+    scrolledLeft = termCount*cellSize - maxCols*cellSize;
+  } //TODO examine this ^
+  if(scrolledLeft < 0) {
+    scrolledLeft = 0;
+  }
+  if(scrolledTop < 0) {
+    scrolledTop = 0;
+  }
+
+  if((init || Math.floor(scrolledLeft/cellSize) != drawnCols || Math.floor(scrolledTop/cellSize) != drawnRows)) {
+    drawnCols = Math.floor(scrolledLeft/cellSize);
+    drawnRows = Math.floor(scrolledTop/cellSize);
+    
+    ontMap.fillStyle = "#FFFFFF";
+    ontMap.fillRect(0,0,1100,500);
+    startXCell = Math.floor(scrolledLeft/cellSize);
+    startYCell = Math.floor(scrolledTop/cellSize);
+
+    for(var c=startXCell; (c<cellData.length) && ((c-startYCell)<maxRows); c++) {
+      for(var s=startXCell; (s<termCount) && ((s-startXCell)<maxCols); s++) {
+	var redcolor = "00";
+	var bluecolor = "00";
+	var greencolor = "00";
+	if(cellData[c][s] == 0) {
+	  redcolor = "FF";
+	  greencolor = "FF";
+	  bluecolor = "FF";
+	  }
+	else {
+	var redfrequency = Math.floor((s / termCount) * 255);
+	redcolor = redfrequency.toString(16);
+	var bluefrequency = 255 - redfrequency;
+	bluecolor = bluefrequency.toString(16);
+	var greenfrequency = redfrequency;
+	greencolor = greenfrequency.toString(16);
+	}
+	if(redcolor.length < 2) {
+	  redcolor = "0" + redcolor;
+	  }
+	if(bluecolor.length < 2) {
+	  bluecolor = "0" + bluecolor;
+	}
+	if(greencolor.length < 2) {
+	  greencolor = "0" + greencolor;
+	}
+	var xCoord = leftOffset+(s-startXCell+.5)*cellSize;
+	var yCoord = topOffset+(c-startYCell)*cellSize;
+	alert(startYCell);
+	ontMap.fillStyle= "#" + redcolor + greencolor + bluecolor;
+	ontMap.fillRect(xCoord, yCoord, cellSize, cellSize);
+	ontMap.fillStyle= "#FFFFFF";
+	ontMap.strokeRect(xCoord-borderWidth/2, yCoord-borderWidth/2,cellSize,cellSize);
+      }
+    }
+    drawTerms(startXCell);
+    drawGenes(startYCell);
+  }
+}
+
+drawMap(true);
+
 
 
 </script>
 
 </body>
-</html> 
+</html>
+<!--
+Time out problem
+General Optimization
+Color
+Scrolling
+-->