Changeset 5138
Legend:
- Unmodified
- Added
- Removed
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trunk/src/clients/web/net/sf/basedb/clients/web/servlet/ExperimentExplorerPlotServlet.java
r5114 r5138 34 34 import java.util.ArrayList; 35 35 import java.util.Collection; 36 import java.util.Collections; 36 37 import java.util.HashMap; 37 38 import java.util.List; … … 40 41 41 42 import javax.imageio.ImageIO; 43 import javax.servlet.ServletConfig; 42 44 import javax.servlet.ServletException; 43 45 import javax.servlet.http.HttpServlet; … … 56 58 import org.jfree.chart.plot.CategoryPlot; 57 59 import org.jfree.chart.plot.Plot; 60 import org.jfree.chart.renderer.category.BoxAndWhiskerRenderer; 58 61 import org.jfree.chart.renderer.category.LineAndShapeRenderer; 59 62 import org.jfree.chart.title.TextTitle; 60 63 import org.jfree.data.category.DefaultCategoryDataset; 64 import org.jfree.data.statistics.BoxAndWhiskerItem; 65 import org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset; 61 66 62 67 import net.sf.basedb.clients.web.ExperimentExplorer; … … 89 94 90 95 /** 91 96 Plot servlet for generating plots from experiment explorer. 97 92 98 @author Nicklas 93 99 @version 2.14 … … 98 104 { 99 105 106 private static final long serialVersionUID = -445763412868957935L; 100 107 private int maxWidth = 1000; 101 108 private int maxHeight = 800; … … 104 111 private String defaultFormat = "png"; 105 112 113 @Override 114 public void init() 115 throws ServletException 116 { 117 ServletConfig cfg = getServletConfig(); 118 maxWidth = Values.getInt(cfg.getInitParameter("maxWidth"), maxWidth); 119 maxHeight = Values.getInt(cfg.getInitParameter("maxHeight"), maxHeight); 120 defaultWidth = Values.getInt(cfg.getInitParameter("defaultWidth"), defaultWidth); 121 defaultHeight = Values.getInt(cfg.getInitParameter("defaultHeight"), defaultHeight); 122 defaultFormat = Values.getString(cfg.getInitParameter("defaultFormat"), defaultFormat); 123 } 106 124 125 @SuppressWarnings("unchecked") 126 @Override 107 127 public void doGet(HttpServletRequest request, HttpServletResponse response) 108 128 throws IOException, ServletException … … 114 134 final int reporterIndex = Values.getInt(request.getParameter("reporterIndex")); 115 135 final int positionIndex = Values.getInt(request.getParameter("positionIndex")); 136 final String plotType = Values.getString(request.getParameter("type"), "line"); 116 137 117 138 // Where to deliver the image … … 150 171 if (yLog && yLabel != null) yLabel = "log2("+yLabel+")"; 151 172 final boolean showXLabels = Values.getBoolean(request.getParameter("showXLabels")); 152 System.out.println("showXLabels=" + showXLabels); 153 173 174 // Box plot specific parameters 175 final int annotationTypeId = Values.getInt(request.getParameter("annotationTypeId")); 176 154 177 final SessionControl sc = Application.getSessionControl(ID, request.getRemoteAddr()); 155 178 DbControl dc = null; … … 165 188 final ExperimentExplorer explorer = ExperimentExplorer.getExplorer(bioAssaySet); 166 189 167 // Load bioassay information - make sure each the labels are unique168 // and that we can go between label<-->column in both directions169 Map<String, Short> labelToColumn = new HashMap<String, Short>();170 Map<Short, String> columnToLabel = new HashMap<Short, String>();171 for (BioAssay ba : bioAssaySet.getBioAssays().list(dc))172 {173 String lbl = ba.getName();174 short column = ba.getDataCubeColumnNo();175 if (labelToColumn.containsKey(lbl))176 {177 lbl = lbl + "-" + ba.getId();178 }179 labelToColumn.put(lbl, column);180 columnToLabel.put(column, lbl);181 }182 190 183 // Load annotation summaries 184 Set<Integer> annotationTypes = explorer.getAnnotationTypeIds(); 185 List<AnnotationSummary> summaries = new ArrayList<AnnotationSummary>(3); 186 if (showXLabels && annotationTypes != null && annotationTypes.size() > 0) 187 { 188 for (Integer annotationTypeId : annotationTypes) 189 { 190 AnnotationType at = AnnotationType.getById(dc, annotationTypeId); 191 summaries.add(explorer.getAnnotationSummary(dc, at)); 192 if (summaries.size() == 3) break; 193 } 194 } 195 191 // Create some common items used for all plot types 192 NumberAxis valueAxis = new NumberAxis(yLabel); 193 CategoryAxis categoryAxis = new CategoryAxis(); 194 196 195 // Convert formulas to Expression:s 197 196 Expression y = yFormula == null ? null : … … 203 202 DynamicSpotQuery query = explorer.getSpotQuery(dc, reporterIndex, positionIndex, new ArrayList<TableColumn>()); 204 203 query.select(Selects.expression(y, "y")); 205 206 // Load the spot data into the dataset 207 DefaultCategoryDataset dataset = new DefaultCategoryDataset(); 208 DynamicResultIterator it = query.iterate(dc); 209 int valueIndex = it.getIndex("y"); 210 int columnIndex = it.getIndex(VirtualColumn.COLUMN.getName()); 211 int posIndex = positionIndex == ExperimentExplorer.SPOT_ALL ? 212 it.getIndex(VirtualColumn.POSITION.getName()) : 0; 213 while (it.hasNext()) 214 { 215 SqlResult result = it.next(); 216 Float value = result.getFloat(valueIndex); 217 short column = result.getShort(columnIndex); 218 int position = posIndex > 0 ? result.getInt(posIndex) : 0; 219 dataset.addValue((Number)value, position, columnToLabel.get(column)); 220 } 221 222 // Create the plot and chart objects 223 NumberAxis valueAxis = new NumberAxis(yLabel); 224 CategoryAxis bioAssayAxis = new CategoryAxis(); 225 bioAssayAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_90); 226 bioAssayAxis.setVisible(showXLabels); 227 Plot plot = new CategoryPlot(dataset, bioAssayAxis, valueAxis, new LineAndShapeRenderer()); 228 JFreeChart chart = new JFreeChart(plot); 204 205 String[] categoryAnnotations = null; 206 207 JFreeChart chart = null; 208 if ("box".equals(plotType)) 209 { 210 // Collect all spot data values in one list per annotation group 211 Map<AnnotationGroup, List<Float>> valuesPerGroup = new HashMap<AnnotationGroup, List<Float>>(); 212 AnnotationType at = AnnotationType.getById(dc, annotationTypeId); 213 AnnotationSummary summary = explorer.getAnnotationSummary(dc, at); 214 DynamicResultIterator it = query.iterate(dc); 215 int valueIndex = it.getIndex("y"); 216 int columnIndex = it.getIndex(VirtualColumn.COLUMN.getName()); 217 int posIndex = positionIndex == ExperimentExplorer.SPOT_ALL ? 218 it.getIndex(VirtualColumn.POSITION.getName()) : 0; 219 while (it.hasNext()) 220 { 221 SqlResult result = it.next(); 222 Float value = result.getFloat(valueIndex); 223 if (value == null || value.isNaN()) continue; 224 short column = result.getShort(columnIndex); 225 AnnotationGroup grp = summary.getAnnotationGroup(column); 226 List<Float> values = valuesPerGroup.get(grp); 227 if (values == null) 228 { 229 values = new ArrayList<Float>(); 230 valuesPerGroup.put(grp, values); 231 } 232 values.add(value); 233 } 234 235 // Create the JFreeChart box-and-whisker dataset 236 DefaultBoxAndWhiskerCategoryDataset dataset = new DefaultBoxAndWhiskerCategoryDataset(); 237 for (AnnotationGroup grp : summary.getAnnotationGroups()) 238 { 239 List<Float> values = valuesPerGroup.get(grp); 240 if (values == null || values.size() == 0) continue; 241 Collections.sort(values); 242 BoxAndWhiskerItem box = calculateBoxAndWhiskerStatistics(values); 243 dataset.add(box, "", new ColumnKey(grp.hashCode(), grp.getTitle())); 244 } 245 categoryAxis.setLabel(at.getName()); 246 BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer(); 247 renderer.setMeanVisible(false); 248 renderer.setMedianVisible(true); 249 renderer.setFillBox(false); 250 renderer.setAutoPopulateSeriesPaint(false); 251 renderer.setBasePaint(Color.BLACK); 252 renderer.setBaseOutlinePaint(Color.BLACK); 253 Plot plot = new CategoryPlot(dataset, categoryAxis, valueAxis, renderer); 254 chart = new JFreeChart(plot); 255 } 256 else if ("line".equals(plotType)) 257 { 258 // Load annotation summaries 259 Set<Integer> annotationTypes = explorer.getAnnotationTypeIds(); 260 List<AnnotationSummary> summaries = new ArrayList<AnnotationSummary>(3); 261 if (showXLabels && annotationTypes != null && annotationTypes.size() > 0) 262 { 263 categoryAnnotations = new String[Math.min(3, annotationTypes.size())]; 264 int i = 0; 265 for (Integer atId : annotationTypes) 266 { 267 AnnotationType at = AnnotationType.getById(dc, atId); 268 summaries.add(explorer.getAnnotationSummary(dc, at)); 269 categoryAnnotations[i] = at.getName(); 270 ++i; 271 if (summaries.size() == 3) break; 272 } 273 } 274 275 // Load bioassay information and related annotation group summaries 276 Map<Short, ColumnKey> columnToLabel = new HashMap<Short, ColumnKey>(); 277 for (BioAssay ba : bioAssaySet.getBioAssays().list(dc)) 278 { 279 short column = ba.getDataCubeColumnNo(); 280 ColumnKey key = new ColumnKey(ba.getId(), ba.getName()); 281 for (AnnotationSummary summary : summaries) 282 { 283 AnnotationGroup grp = summary.getAnnotationGroup(column); 284 if (grp != null) key.setColor(summary.getAnnotationType().getName(), grp.getAwtColor()); 285 } 286 columnToLabel.put(column, key); 287 } 288 289 // Load the spot data into the dataset 290 DefaultCategoryDataset dataset = new DefaultCategoryDataset(); 291 DynamicResultIterator it = query.iterate(dc); 292 int valueIndex = it.getIndex("y"); 293 int columnIndex = it.getIndex(VirtualColumn.COLUMN.getName()); 294 int posIndex = positionIndex == ExperimentExplorer.SPOT_ALL ? 295 it.getIndex(VirtualColumn.POSITION.getName()) : 0; 296 while (it.hasNext()) 297 { 298 SqlResult result = it.next(); 299 Float value = result.getFloat(valueIndex); 300 if (value == null || value.isNaN()) continue; 301 short column = result.getShort(columnIndex); 302 int position = posIndex > 0 ? result.getInt(posIndex) : 0; 303 dataset.addValue((Number)value, position, columnToLabel.get(column)); 304 } 305 306 // Create the plot and chart objects 307 categoryAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_90); 308 categoryAxis.setVisible(showXLabels); 309 Plot plot = new CategoryPlot(dataset, categoryAxis, valueAxis, new LineAndShapeRenderer()); 310 chart = new JFreeChart(plot); 311 } 229 312 chart.removeLegend(); 230 313 if (title != null) chart.setTitle(title); … … 235 318 ChartRenderingInfo chartInfo = null; 236 319 int chartHeight = height; 237 if ( summaries.size() > 0)320 if (categoryAnnotations != null) 238 321 { 239 322 chartEntities = new StandardEntityCollection(); 240 323 chartInfo = new ChartRenderingInfo(chartEntities); 241 chartHeight -= 15 * summaries.size(); 242 324 chartHeight -= 15 * categoryAnnotations.length; 243 325 } 244 326 BufferedImage temp = chart.createBufferedImage(width, chartHeight, chartInfo); 245 if (summaries.size() == 0) 246 { 327 if (categoryAnnotations == null) 328 { 329 // Use the image that JFreeChart generated if we don't have any annotations 247 330 image = temp; 248 331 } 249 332 else 250 333 { 334 // Otherwise... create a new (bigger) image... 251 335 image = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); 252 336 Graphics2D g = image.createGraphics(); … … 254 338 g.clearRect(0, 0, width, height); 255 339 g.setColor(Color.BLACK); 340 // ... and copy the image from JFreeChart into it 256 341 g.drawImage(temp, 0, 0, width, chartHeight, 0, 0, width, chartHeight, null); 342 343 // Draw annotation color rectangles 257 344 int minX = width; 258 for (ChartEntity c : (Collection<ChartEntity>)chartEntities.getEntities())259 { 260 if (c .getClass() == CategoryLabelEntity.class)345 for (ChartEntity chartEntity : (Collection<ChartEntity>)chartEntities.getEntities()) 346 { 347 if (chartEntity.getClass() == CategoryLabelEntity.class) 261 348 { 262 CategoryLabelEntity lbl = (CategoryLabelEntity)c; 349 // This is the category (x) axis label object 350 CategoryLabelEntity lbl = (CategoryLabelEntity)chartEntity; 351 // Get the coordinates for the label 352 Rectangle lblCoordinates = chartEntity.getArea().getBounds(); 353 if (lblCoordinates.getMinX() < minX) minX = (int)lblCoordinates.getMinX(); 354 355 ColumnKey key = (ColumnKey)lbl.getKey(); 263 356 int currentY = chartHeight; 264 for ( AnnotationSummary summary : summaries)357 for (String annotation : categoryAnnotations) 265 358 { 266 AnnotationGroup grp = summary.getAnnotationGroup(labelToColumn.get(lbl.getKey()));267 if ( grp!= null)359 Color color = key.getColor(annotation); 360 if (color != null) 268 361 { 269 Rectangle r = c.getArea().getBounds(); 270 if (r.getMinX() < minX) minX = (int)r.getMinX(); 271 Rectangle r2 = new Rectangle((int)r.getMinX(), currentY, (int)r.getWidth(), 10); 272 g.setColor(grp.getAwtColor()); 273 g.fill(r2); 362 // Draw colored rectangles below the label 363 Rectangle r = new Rectangle((int)lblCoordinates.getMinX(), currentY, (int)lblCoordinates.getWidth(), 10); 364 g.setColor(color); 365 g.fill(r); 274 366 g.setColor(Color.LIGHT_GRAY); 275 g.draw(r 2);367 g.draw(r); 276 368 } 277 369 currentY += 15; … … 281 373 // Draw annotation titles 282 374 int currentY = chartHeight + 10; 283 g.setPaint( bioAssayAxis.getLabelPaint());375 g.setPaint(categoryAxis.getLabelPaint()); 284 376 g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); 285 286 Font lblFont = bioAssayAxis.getLabelFont(); 377 Font lblFont = categoryAxis.getLabelFont(); 287 378 FontRenderContext context = g.getFontRenderContext(); 288 bioAssayAxis.getLabelInsets(); 289 290 for (AnnotationSummary summary : summaries)291 {292 String lbl = summary.getAnnotationType().getName();293 Rectangle2D bounds = lblFont.getStringBounds( lbl, context);379 380 for (String annotation : categoryAnnotations) 381 { 382 // Try to calculate coordinate so that the text is right-aligned 383 // near the first label 384 Rectangle2D bounds = lblFont.getStringBounds(annotation, context); 294 385 int x = minX - (int)bounds.getWidth() - 5; 295 386 if (x < 0) 296 387 { 297 388 x = 0; 298 lbl = StringUtil.trimString(lbl, (int)(lbl.length() * minX / bounds.getWidth()));389 annotation = StringUtil.trimString(annotation, (int)(annotation.length() * minX / bounds.getWidth())); 299 390 } 300 g.drawString( lbl, x, currentY);391 g.drawString(annotation, x, currentY); 301 392 currentY += 15; 302 393 } … … 386 477 } 387 478 479 /** 480 Creates a box-and-whisker data holder for the given list of values. 481 The data holder will be populated with the median and the 5th, 25th, 75th and 482 95th percentile values as follows: 483 <ul> 484 <li>median = BAWI.getMedian() 485 <li>5th percentile = BAWI.getMinRegularValue() 486 <li>25th percentile = BAWI.getQ1() 487 <li>75th percentile = BAWI.getQ3() 488 <li>95th percentile = BAWI.getMaxRegularValue() 489 </ul> 490 The mean and outlier values are currently not calculated (may change in 491 the future). 492 493 @param values The list of values which must be sorted in ascending order 494 @return A BoxAndWhiskerItem object 495 */ 496 public BoxAndWhiskerItem calculateBoxAndWhiskerStatistics(List<Float> values) 497 { 498 float median = getPercentile(values, 50); 499 float p5 = getPercentile(values, 5); 500 float p25 = getPercentile(values, 25); 501 float p75 = getPercentile(values, 75); 502 float p95 = getPercentile(values, 95); 503 return new BoxAndWhiskerItem(Float.NaN, median, p25, p75, p5, p95, Float.NaN, Float.NaN, null); 504 } 505 506 /** 507 Calculates the percentile values from a sorted list of values. 508 If the percentile falls between two elements in the list the 509 average of the two nearest elements are used. 510 511 @param values The values which must be sorted 512 @param percentile The percentile, a value between 0 and 100 513 @return The percentile value, or Float.NaN if it could not be 514 calculated 515 */ 516 public float getPercentile(List<? extends Number> values, int percentile) 517 { 518 int size = values.size(); 519 if (size == 0) return Float.NaN; 520 if (size == 1) return values.get(0).floatValue(); 521 522 int width = size + 1; 523 int pos = width * percentile / 100; 524 if (pos == 0) 525 { 526 // Overflow to the left -- return first value 527 return values.get(0).floatValue(); 528 } 529 else if (pos >= size) 530 { 531 // Overflow to the right -- return last value 532 return values.get(size-1).floatValue(); 533 } 534 535 if (width * percentile % 100 == 0) 536 { 537 // Exact hit -- return one value 538 return values.get(pos-1).floatValue(); 539 } 540 else 541 { 542 // Hit between two values -- return the average 543 return (values.get(pos-1).floatValue() + values.get(pos).floatValue())/2; 544 } 545 } 546 547 /** 548 Uses as a column key in the plots. This allows us to 549 separate the displayed label from the identity of the column. 550 Eg. there is no need to make sure that the label strings are unique 551 since we can use some internal id for this purpose. 552 <p> 553 Additionally, this class allows us to map annotations to colors 554 that are used to draw small colored boxes below each column label. 555 */ 556 public static class ColumnKey 557 implements Comparable<ColumnKey> 558 { 559 private final Comparable id; 560 private final String title; 561 private final Map<String, Color> annotations; 562 563 public ColumnKey(Comparable id, String title) 564 { 565 this.id = id; 566 this.title = title; 567 this.annotations = new HashMap<String, Color>(); 568 } 569 570 /* 571 From the Comparable interface 572 ----------------------------- 573 */ 574 /** 575 The ID of the key determines equality. 576 */ 577 @SuppressWarnings("unchecked") 578 @Override 579 public int compareTo(ColumnKey o) 580 { 581 return id.compareTo(o.id); 582 } 583 // ------------------------------- 584 585 /* 586 From the Object class 587 ------------------------------- 588 */ 589 @Override 590 public String toString() 591 { 592 return title; 593 } 594 595 @Override 596 public boolean equals(Object o) 597 { 598 if (o == null) return false; 599 if (this == o) return true; 600 if (o.getClass() != getClass()) return false; 601 ColumnKey ck = (ColumnKey)o; 602 return id.equals(ck.id); 603 } 604 605 @Override 606 public int hashCode() 607 { 608 return id.hashCode(); 609 } 610 // ------------------------------------ 611 612 public void setColor(String annotation, Color color) 613 { 614 annotations.put(annotation, color); 615 } 616 617 public Color getColor(String annotation) 618 { 619 return annotations.get(annotation); 620 } 621 622 } 623 388 624 } -
trunk/www/views/experiments/explorer/view/plotter.jsp
r5114 r5138 74 74 final int reporterIndex = Values.getInt(request.getParameter("reporterIndex")); 75 75 final int positionIndex = Values.getInt(request.getParameter("positionIndex")); 76 final String plotType = Values.getString(request.getParameter("type"), "line"); 77 final int annotationTypeId = Values.getInt(request.getParameter("annotationTypeId")); 76 78 final boolean needAverageMethod = positionIndex == ExperimentExplorer.SPOT_AVG; 77 79 78 BioAssaySet bas = BioAssaySet.getById(dc, bioAssaySetId); 79 RawDataType rdt = bas.getRawDataType(); 80 Experiment experiment = bas.getExperiment(); 81 int maxRawMappings = bas.getMaxRawMappingsForSpot(); 82 IntensityTransform transform = bas.getIntensityTransform(); 80 final BioAssaySet bas = BioAssaySet.getById(dc, bioAssaySetId); 81 final RawDataType rdt = bas.getRawDataType(); 82 final Experiment experiment = bas.getExperiment(); 83 final int maxRawMappings = bas.getMaxRawMappingsForSpot(); 84 final IntensityTransform transform = bas.getIntensityTransform(); 85 final ExperimentExplorer explorer = ExperimentExplorer.getExplorer(bas); 86 final List<AnnotationType> annotationTypes = explorer.getAnnotationTypes(dc, true); 83 87 84 88 List<TableColumn> formulas = new LinkedList<TableColumn>(); … … 131 135 { 132 136 var plotType = getPlotType(); 133 if (plotType == 'scatter') 134 { 135 return validateScatterPlot(); 137 if (plotType == 'line') 138 { 139 return validateLinePlot(); 140 } 141 else if (plotType == 'box') 142 { 143 return validateBoxPlot(); 136 144 } 137 145 return false; 138 146 } 139 function validateScatterPlot() 140 { 141 var frm = document.forms['scatter']; 147 148 function validateLinePlot() 149 { 150 var frm = document.forms['line']; 142 151 if (Main.trimString(frm.yFormula.value) == '') 143 152 { … … 149 158 } 150 159 151 var plotType = 'scatter'; 160 function validateBoxPlot() 161 { 162 var frm = document.forms['box']; 163 if (Main.trimString(frm.yFormula.value) == '') 164 { 165 alert("You must enter an expression for the Y axis"); 166 frm.yFormula.focus(); 167 return false; 168 } 169 return true; 170 } 171 172 var plotType = '<%=plotType%>'; 152 173 function getPlotType() 153 174 { … … 157 178 function switchTab(tabControlId, tabId) 158 179 { 159 if (tabId == ' scatter' || tabId == 'histogram')180 if (tabId == 'line' || tabId == 'box') 160 181 { 161 182 plotType = tabId; … … 167 188 { 168 189 var index = list.selectedIndex; 169 var frm = document.forms['scatter'];190 var frm = list.form; 170 191 if (frm.averageMethod) 171 192 { … … 193 214 url += '&height='+plotFrm.height.value; 194 215 } 195 196 216 var plotType = getPlotType(); 197 if (plotType == ' scatter')198 { 199 var frm = document.forms[' scatter'];200 url += '&type= scatter';217 if (plotType == 'line') 218 { 219 var frm = document.forms['line']; 220 url += '&type=line'; 201 221 url += '&y='+Main.encodeURI(frm.yFormula.value); 202 222 url += '&yLog='+(frm.yLog.checked ? 1 : 0); … … 207 227 url += '&averageMethod=' + frm.averageMethod[frm.averageMethod.selectedIndex].value; 208 228 } 229 } 230 else if (plotType == 'box') 231 { 232 var frm = document.forms['box']; 233 url += '&type=box'; 234 url += '&y='+Main.encodeURI(frm.yFormula.value); 235 url += '&yLog='+(frm.yLog.checked ? 1 : 0); 236 url += '&yLabel='+Main.encodeURI(frm.yLabel.value); 237 url += '&annotationTypeId=' + frm.annotationTypeId[frm.annotationTypeId.selectedIndex].value; 209 238 } 210 239 url += '&' + new Date().getTime(); … … 326 355 style="<%="width: "+(int)(scale*340)+"px;"%>" 327 356 contentstyle="<%="height: "+(int)(scale*340)+"px;"%>" 357 active="<%=plotType%>" remember="false" 328 358 switch="switchTab"> 329 <t:tab id=" scatter" title="Scatter plot" helpid="plotter.scatterplot"330 tooltip="Create a scatter plot">331 <form name=" scatter">359 <t:tab id="line" title="Line plot" helpid="explorer.lineplot" 360 tooltip="Create a line plot with bioassays along the x axis"> 361 <form name="line"> 332 362 <table border="0" cellspacing="0" cellpadding="2" class="form"> 333 363 <tr> … … 353 383 image="expression_builder.gif" 354 384 tooltip="Use the Expression builder" 355 onclick="openExpressionBuilder('Y-axis expression', ' scatter', 'yFormula', 'COLUMN_EXPRESSION')"385 onclick="openExpressionBuilder('Y-axis expression', 'line', 'yFormula', 'COLUMN_EXPRESSION')" 356 386 /> 357 387 </td> … … 398 428 </table> 399 429 </form> 400 </t:tab> 430 </t:tab> 431 <t:tab id="box" title="Box plot" helpid="explorer.boxplot" 432 tooltip="Create a box plot with annotation values along the x axis"> 433 <form name="box"> 434 <table border="0" cellspacing="0" cellpadding="2" class="form"> 435 <tr> 436 <td class="prompt" colspan="3">Y-axis</td> 437 </tr> 438 <tr> 439 <td> Presets</td> 440 <td colspan="2"> 441 <select name="yPresets" style="width: 20em;" 442 onchange="presetOnChange(this, this.form.yFormula, this.form.yLabel)" 443 > 444 <option value="">- select from list or enter formula below - 445 <%=formulaOptions.toString()%> 446 </select> 447 </td> 448 </tr> 449 <tr> 450 <td> Expression</td> 451 <td><input type="text" class="text required" size="30" maxlength="255" name="yFormula"></td> 452 <td> 453 <base:button 454 title="" 455 image="expression_builder.gif" 456 tooltip="Use the Expression builder" 457 onclick="openExpressionBuilder('Y-axis expression', 'box', 'yFormula', 'COLUMN_EXPRESSION')" 458 /> 459 </td> 460 </tr> 461 <tr> 462 <td> Label</td> 463 <td colspan="2"><input type="text" class="text" size="30" maxlength="255" name="yLabel"></td> 464 </tr> 465 <tr> 466 <td> Log scale</td> 467 <td colspan="2"><input type="checkbox" name="yLog" value="1"></td> 468 </tr> 469 <% 470 if (positionIndex == ExperimentExplorer.SPOT_AVG) 471 { 472 %> 473 <tr> 474 <td> Average</td> 475 <td> 476 <select name="averageMethod"> 477 <% 478 for (Formula.AverageMethod method : Formula.AverageMethod.values()) 479 { 480 if (method != Formula.AverageMethod.NONE) 481 { 482 %> 483 <option value="<%=method.name()%>"><%=method.toString()%></option> 484 <% 485 } 486 } 487 %> 488 </select> 489 </td> 490 <% 491 } 492 %> 493 <tr> 494 <td class="prompt" colspan="3">X-axis</td> 495 </tr> 496 <tr> 497 <td> Annotation</td> 498 <td> 499 <select name="annotationTypeId"> 500 <% 501 for (AnnotationType at : annotationTypes) 502 { 503 String selected = at.getId() == annotationTypeId ? "selected" : ""; 504 %> 505 <option value="<%=at.getId()%>" <%=selected%>><%=HTML.encodeTags(at.getName())%> 506 <% 507 } 508 %> 509 </select> 510 </td> 511 </tr> 512 </table> 513 </form> 514 </t:tab> 401 515 </t:tabcontrol> 402 516 </td> -
trunk/www/views/experiments/explorer/view/view.jsp
r5137 r5138 256 256 function plotSpotData() 257 257 { 258 var url = 'plotter.jsp?ID=<%=ID%> ';258 var url = 'plotter.jsp?ID=<%=ID%>&type=line'; 259 259 url += '&bioAssaySetId=<%=bioAssaySetId%>'; 260 260 url += '&reporterIndex=<%=reporterIndex%>'; 261 261 url += '&positionIndex=<%=positionIndex%>'; 262 262 Main.openPopup(url, 'SpotPlot', 1100, 700); 263 } 264 function boxPlot(annotationType) 265 { 266 var url = 'plotter.jsp?ID=<%=ID%>&type=box'; 267 url += '&bioAssaySetId=<%=bioAssaySetId%>'; 268 url += '&reporterIndex=<%=reporterIndex%>'; 269 url += '&positionIndex=<%=positionIndex%>'; 270 url += '&annotationTypeId=' + annotationType; 271 Main.openPopup(url, 'BoxPlot', 1100, 700); 263 272 } 264 273 </script> … … 458 467 <tr> 459 468 <td class="summaryheader"><%=Base.getLinkedName(ID, at, false, true)%></td> 469 <td class="summaryheader"><base:icon 470 image="plotter.gif" 471 onclick="<%="boxPlot(" + at.getId() + ")"%>" 472 tooltip="Box plot for selected spot data per annotation group" 473 /></td> 460 474 <% 461 475 for (AnnotationGroup ag : summary.getAnnotationGroups()) … … 474 488 %> 475 489 <tr> 476 <td >Mean ch <%=ch%> int.</td>490 <td colspan="2">Mean ch <%=ch%> int.</td> 477 491 <% 478 492 for (AnnotationGroup ag : summary.getAnnotationGroups()) … … 490 504 %> 491 505 <tr> 492 <td title="The geometric mean of the ratios">G. mean ratio</td>506 <td colspan="2" title="The geometric mean of the ratios">G. mean ratio</td> 493 507 <% 494 508 for (AnnotationGroup ag : summary.getAnnotationGroups()) … … 501 515 </tr> 502 516 <tr> 503 <td title="Standard deviation of log2 ratios">log2ratio SD</td>517 <td colspan="2" title="Standard deviation of log2 ratios">log2ratio SD</td> 504 518 <% 505 519 for (AnnotationGroup ag : summary.getAnnotationGroups()) … … 512 526 </tr> 513 527 <tr> 514 <td title="The number of spots falling in this group">Count</td>528 <td colspan="2" title="The number of spots falling in this group">Count</td> 515 529 <% 516 530 for (AnnotationGroup ag : summary.getAnnotationGroups())
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