List Analysis for A.thaliana Senescence (0 Genes)

ent.name MRNA.cufflinksscores.experiment.experimentGroup MRNA.cufflinksscores.abundance MRNA.cufflinksscores.conflo MRNA.cufflinksscores.confhi" sortOrder="MRNA.primaryIdentifier asc" constraintLogic="A and B">'+ ''+featureConstraint+''+ ''+conditionConstraint+''; var encodedQuery = encodeURIComponent(query); encodedQuery = encodedQuery.replace("%20", "+"); window.open("/phytomine/loadQuery.do?skipBuilder=true&query=" + encodedQuery + "&method=xml"); } else { alert("Unexpected expression type: gene"); } }}); // cluster on gene/mrnas if (feature_count > max_cluster) { jQuery("#fpkmHierarchical").attr('disabled', true); } if (organism_count > 1) { jQuery("#fpkmHierarchical").attr('disabled', true); } // cluster on gene/mrnas if (feature_count > max_cluster) { jQuery("#fpkmHierarchical").attr('disabled', true); } if (organism_count > 1) { jQuery("#fpkmHierarchical").attr('disabled', true); } if (experiment_count > 3 && experiment_count <= max_cluster) { fpkmHeatMap.clusterSamples(); fpkmHeatMap.kmeansSamples(); for (var i=4; i < experiment_count; ++i) { jQuery('#fpkmKMeans'). append(jQuery(""). attr("value",i). text(i)); } } else { jQuery("#fpkmKMeans").attr('disabled', true); } // cluster on conditions if (experiment_count <= max_cluster) { fpkmHeatMap.clusterVariables(); // clustering method will call draw action within it. fpkmHeatMap.draw(); } // cx_cellline.kmeansVariables(); // fpkmHeatMap.draw(); jQuery('#fpkmHierarchical').change(function() { fpkmHeatMap.linkage = this.value; if (feature_count >= 3) { fpkmHeatMap.clusterSamples(); } fpkmHeatMap.clusterVariables(); fpkmHeatMap.draw(); }); jQuery('#fpkmKMeans').change(function() { fpkmHeatMap.kmeansClusters = parseInt(this.value); fpkmHeatMap.kmeansSamples(); // fpkmHeatMapcl.kmeansVariables(); fpkmHeatMap.draw(); }); // the correlation map // but remove things with zero variance var parsedJSON = JSON.parse('{}') var newFPKM = []; var newVars = []; for ( i=0; i < parsedJSON.y.data.length; i++) { var fpkm = parsedJSON.y.data[i]; var vars = parsedJSON.y.vars[i]; var sum1 = 0; var sum2 = 0; for( j=0; j 1e-4) { newFPKM.push(fpkm); newVars.push(vars); } } var newJSON = new Object(); newJSON.y = new Object(); newJSON.y.data = newFPKM; newJSON.y.vars = newVars; newJSON.y.smps = parsedJSON.y.smps; newJSON.y.desc = parsedJSON.y.desc; var correlationHeatMap = new CanvasXpress('canvas_corr', newJSON, {'graphType': 'Correlation', 'correlationAxis' : "variables", 'gradient': true} ); }