From fd57492fdfeb83134b7271fa75425c8028c380f4 Mon Sep 17 00:00:00 2001 From: miles Date: Mon, 19 Nov 2012 23:33:11 +0000 Subject: [PATCH] Fixed species inclusion to show even irrelevant species if asked. Improved summary of data. svn path=/; revision=415 --- Personnel/miles/Web Page/Heatmap.jar | Bin 582458 -> 582469 bytes Personnel/miles/Web Page/heatMap.php | 105 +++++++++++++-------------- Personnel/miles/Web Page/upload.php | 2 +- 3 files changed, 52 insertions(+), 55 deletions(-) diff --git a/Personnel/miles/Web Page/Heatmap.jar b/Personnel/miles/Web Page/Heatmap.jar index 7b1c94267f596e946dd02353ae6483689d813368..855ba426799b1f12fc63ed538e94980e6ea0a753 100644 GIT binary patch delta 11539 zcmYjX1z1$w(+3uIFAWMvNQ)>bN~<6sA(Dbf*GnTPspO(G2$C)#ogyi5NhxV*B?P1e zq*FoE@9y1w-|zqUJnrxQX3orV7c8#wS!9duoSpdgG)^oz3w4?}D#$W@e^r?s<#nPBv$Rb8FA7HIi zX^26=np16BWH1ow-@#eq91_E=75PQThp8<9m?~e7%HjevGb84}XcYitmB8{!7;IBQ z08fGEoeB4G+Xl`-Tf?ehVj>C2LFLDU)UW_Fa3PF?cMooP5Qf1)fnI3BNH{ehDumFO z1Zy;Y*O(JS?MX<7*(d_Iz@|t-Tihz%7(#Vi_FgL@{@(=|X7DY51S=8<{cN!7K`3;3 zTqts32oBKxlrSBBj2AZJ#55NJ44~W}!b1SwK-PI85zqle)CVU713%hR6Nyp6mY_#5 zI6*i8881;X94zi}T#zW}e;!|o5_SL2W8`(BC;#&(E>D#9KR!^ZM4Gs=K+$qwXvzRu 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"; //echo $finalInput; - +//echo "

"; exec("java -Djava.awt.headless=true -jar Heatmap.jar " . "\"" . $finalInput . "\"", $output); //main heatmap data parsing @@ -38,16 +37,30 @@ for ($i = 0; $i < sizeof($output); $i ++) { $tmp[$i] = explode(",", $output[$i]); } - -$allSpecies; +$speciesWithData; for ($s = 0; $s < sizeof($tmp) - 2; $s ++) // the last array in tmp is the list of cluster IDs { - $allSpecies[$s] = $tmp[$s][0]; + $speciesWithData[$s] = $tmp[$s][0]; } -if(!isset($originalSpecies)) { -$originalSpecies = $allSpecies; -} +$allSpecies = $speciesWithData; +$j = 0; +for($i = 0; $i < sizeof($includedSpecies); $i++) + { + $included = false; + for($s = 0; $s < sizeof($speciesWithData); $s++) + { + if($includedSpecies[$i] == $speciesWithData[$s]) + { + $included = true; + } + } + if($included == false) + { + $allSpecies[sizeof($allSpecies) + $j] = $includedSpecies[$i]; + $j++; + } + } $allClusterIDs; for ($c = 0; $c < sizeof($tmp[sizeof($tmp) - 2]); $c ++) @@ -55,12 +68,20 @@ for ($c = 0; $c < sizeof($tmp[sizeof($tmp) - 2]); $c ++) $allClusterIDs[$c] = $tmp[sizeof($tmp) - 2][$c]; } - $heatMapData; -for ($s = 0; $s < (sizeof($tmp) - 2); $s ++) +for ($s = 0; $s < sizeof($allSpecies); $s ++) { for ($c = 0; $c < sizeof($allClusterIDs); $c ++) - $heatMapData[$s][$c] = $tmp[$s][$c+1]; + { + if($s < sizeof($speciesWithData)) + { + $heatMapData[$s][$c] = $tmp[$s][$c+1]; + } + else + { + $heatMapData[$s][$c] = 0; + } + } } $geneIDs = explode(" ", $input); @@ -106,50 +127,25 @@ $height = 25 * $clusterCount + 200; ?> -




+

-The following species have been included in the heat map: +The following species have been included in the heat map: +

Click on a species name, cluster number, or cell for more information. -
Scroll down to see more clusters, right to see more species (if any exist). -
- There are " . $speciesCount . " species in the heatmap."; ?> +

Scroll down to see more clusters, right to see more species (if any exist). +

+
- - - - -
@@ -445,7 +441,7 @@ function jumpToCluster() { function generateImage() { document.infoForm.action="download.php"; - document.infoForm.param.value = "unset DISPLAY && java -Djava.awt.headless=true -jar Heatmap.jar \"image" + "" + ";" + "\""; + document.infoForm.param.value = "unset DISPLAY && java -Djava.awt.headless=true -jar Heatmap.jar \"image" + "" + ";" + "\""; document.infoForm.submit(); } @@ -459,6 +455,7 @@ canvas.addEventListener('mouseup', showInfo, false); \ No newline at end of file diff --git a/Personnel/miles/Web Page/upload.php b/Personnel/miles/Web Page/upload.php index af35d80..c63be21 100644 --- a/Personnel/miles/Web Page/upload.php +++ b/Personnel/miles/Web Page/upload.php @@ -37,7 +37,7 @@ else if($goToNode10){ ?> - +