Improved heatmaps, numpy 1.8.1 fixes

Improved heatmaps to allow only active features to be plotted. Fixed
bugs relating to index slicing in numpy 1.8.1.

setup.py

@@ -37,7 +37,7 @@
                   ('.', ['README.md'])]
 setup(
     name='STAMP',
-    version='2.0.6',
+    version='2.0.7',
     author='Donovan Parks, Rob Beiko',
     author_email='[email protected]',
     packages=['stamp', 'stamp.GUI'] + pluginPkgs + metagenomicPkgs,

stamp/STAMP.py

@@ -23,8 +23,8 @@
 __copyright__ = 'Copyright 2013'
 __credits__ = ['Donovan Parks']
 __license__ = 'GPL3'
-__version__ = '2.0.6'
-__date__ = 'July 7, 2014'
+__version__ = '2.0.7'
+__date__ = 'July 26, 2014'
 __maintainer__ = 'Donovan Parks'
 __email__ = '[email protected]'
 __status__ = 'Development'
@@ -1738,7 +1738,7 @@ def updateStatusBar(self):
 
 	def openAboutDlg(self):
 		QtGui.QMessageBox.about(self, 'About...',
-				'STAMP: STatistical Analysis of Metagenomic Profiles\n\n'
+				'STAMP: statistical analysis of taxonomic and functional profiles\n\n'
 				'%s\n'
 				'%s\n'
 				'%s\n\n'

stamp/mainUI.py

@@ -2070,7 +2070,6 @@ def retranslateUi(self, MainWindow):
         self.cboGroupSeqFilter.setItemText(2, _translate("MainWindow", "independent, maximum", None))
         self.cboGroupSeqFilter.setItemText(3, _translate("MainWindow", "independent, minimum", None))
         self.lblGroupSeqFilter1.setText(_translate("MainWindow", "Maximum (<):", None))
-        self.spinGroupFilter1.setStatusTip(_translate("MainWindow", "Filter out all features where sample 2 does not contain more than the specified number of sequences", None))
         self.lblGroupSeqFilter2.setText(_translate("MainWindow", "Group 2 (<):", None))
         self.label_24.setText(_translate("MainWindow", "Parent seq. filter:", None))
         self.cboGroupParentSeqFilter.setItemText(0, _translate("MainWindow", "maximum", None))
@@ -2117,7 +2116,6 @@ def retranslateUi(self, MainWindow):
         self.cboSampleSeqFilter.setItemText(1, _translate("MainWindow", "minimum", None))
         self.cboSampleSeqFilter.setItemText(2, _translate("MainWindow", "independent", None))
         self.lblSampleSeqFilterSample1.setText(_translate("MainWindow", "Maximum (<):", None))
-        self.spinSampleFilterSample1.setStatusTip(_translate("MainWindow", "Filter out all features where sample 2 does not contain more than the specified number of sequences", None))
         self.lblSampleSeqFilterSample2.setText(_translate("MainWindow", "Sample 2 (<):", None))
         self.label_12.setText(_translate("MainWindow", "Parent seq. filter:", None))
         self.cboSampleParentSeqFilter.setItemText(0, _translate("MainWindow", "maximum", None))

stamp/metagenomics/GroupProfile.py

@@ -87,9 +87,12 @@ def getParentFeatureCounts(self, feature):
 		return data1, data2
 
 	def getFeatureCountsAll(self):
+		return self.getActiveFeatureCounts(self.profileDict.keys())
+
+	def getActiveFeatureCounts(self, activeFeatures):
 		seqGroup1 = [] 
 		seqGroup2 = []
-		for feature in self.profileDict.keys():
+		for feature in activeFeatures:
 			data1, data2 = self.getFeatureCounts(feature)
 			seqGroup1.append(data1)
 			seqGroup2.append(data2)
@@ -130,9 +133,12 @@ def getFeatureProportions(self, feature):
 		return data1, data2
 
 	def getFeatureProportionsAll(self):
+		return self.getActiveFeatureProportions(self.profileDict.keys())
+
+	def getActiveFeatureProportions(self, activeFeatures):
 		groupData1 = [] 
 		groupData2 = []
-		for feature in self.profileDict.keys():
+		for feature in activeFeatures:
 			data1, data2 = self.getFeatureProportions(feature)
 			groupData1.append(data1)
 			groupData2.append(data2)

stamp/metagenomics/MultiGroupProfile.py

@@ -152,6 +152,14 @@ def getActiveFeatureCountsAll(self):
 			allData.append(data)
 
 		return allData
+
+	def getActiveFeatureFromActiveSamplesCounts(self, activeFeatures):
+		allData = [] 
+		for feature in activeFeatures:
+			data = self.getActiveFeatureCounts(feature)
+			allData.append(data)
+
+		return allData
 
 	def getParentCounts(self, feature):
 		profile = self.profileDict[feature]
@@ -222,6 +230,14 @@ def getActiveFeatureProportionsAll(self):
 			allData.append(data)
 
 		return allData
+
+	def getActiveFeatureFromActiveSamplesProportions(self, activeFeatures):
+		allData = [] 
+		for feature in activeFeatures:
+			data = self.getActiveFeatureProportions(feature)
+			allData.append(data)
+
+		return allData
 
 	def getFeatureMatrix(self):
 		numSamples = len(self.profileDict[self.profileDict.keys()[0]].featureCounts)

stamp/plugins/groups/plots/HeatmapPlot.py

@@ -58,10 +58,9 @@ def __init__(self, preferences, parent=None):
 		self.name = 'Heatmap plot'
 		self.type = 'Exploratory'
 
-		self.bPlotFeaturesIndividually = False
-
 		self.settings = preferences['Settings']
 		self.fieldToPlot = self.settings.value('group: ' + self.name + '/field to plot', 'Proportion of sequences (%)').toString()
+		self.bPlotOnlyActiveFeatures = self.settings.value('group: ' + self.name + '/plot only active features', False).toBool()
 		self.figWidth = self.settings.value('group: ' + self.name + '/width', 7.0).toDouble()[0]
 		self.figHeight = self.settings.value('group: ' + self.name + '/height', 7.0).toDouble()[0]
 		self.dendrogramMethod = self.settings.value('group: ' + self.name + '/dendrogram method', 'Average neighbour (UPGMA)').toString()
@@ -79,6 +78,7 @@ def mirrorProperties(self, plotToCopy):
 		self.name = plotToCopy.name
 
 		self.fieldToPlot = plotToCopy.fieldToPlot
+		self.bPlotOnlyActiveFeatures = plotToCopy.bPlotOnlyActiveFeatures
 
 		self.figWidth = plotToCopy.figWidth
 		self.figHeight = plotToCopy.figHeight
@@ -115,10 +115,16 @@ def plotDendrogram(self, matrix, axis, clusteringThreshold, orientation, bPlot):
 		return index, dendrogram['leaves']
 
 	def plot(self, profile, statsResults):
-		if len(profile.profileDict) <= 0 or len(profile.samplesInGroup1) == 0 or len(profile.samplesInGroup2) == 0:
+
+		# determine features to plot
+		featuresToPlot = profile.profileDict.keys()
+		if self.bPlotOnlyActiveFeatures:
+			featuresToPlot = statsResults.activeFeatures
+
+		if len(featuresToPlot) <= 1 or (len(profile.samplesInGroup1) + len(profile.samplesInGroup2)) <= 1:
 			self.emptyAxis()
 			return
-		elif len(profile.profileDict) > 100 or len(profile.samplesInGroup1) + len(profile.samplesInGroup2) > 100:
+		elif len(featuresToPlot) > 100 or len(profile.samplesInGroup1) + len(profile.samplesInGroup2) > 100:
 			QtGui.QApplication.instance().setOverrideCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
 			QtGui.QMessageBox.information(self, 'Too much data!', 'Heatmap plots are limited to 100 samples and 100 features.', QtGui.QMessageBox.Ok)
 			QtGui.QApplication.instance().restoreOverrideCursor()
@@ -159,9 +165,9 @@ def plot(self, profile, statsResults):
 
 		# *** Get data for each group
 		if self.fieldToPlot == "Number of sequences":
-			data1, data2 = profile.getFeatureCountsAll()
+			data1, data2 = profile.getActiveFeatureCounts(featuresToPlot)
 		else: # Proportion of sequences (%)
-			data1, data2 = profile.getFeatureProportionsAll()
+			data1, data2 = profile.getActiveFeatureProportions(featuresToPlot)
 
 		matrix = []
 		for row in data1:
@@ -174,7 +180,7 @@ def plot(self, profile, statsResults):
 
 		# *** Get heatmap data
 		colHeaders = profile.samplesInGroup1 + profile.samplesInGroup2
-		rowHeaders = profile.getFeatures()
+		rowHeaders = featuresToPlot 
 
 		# *** Find longest label
 		bTruncate = False
@@ -296,25 +302,27 @@ def plot(self, profile, statsResults):
 
 		sampleColourMap = mpl.colors.ListedColormap(sampleColourMap)
 		matrix = matrix[:,leafIndex2]
-		ind2 = ind2[:,leafIndex2] 
-
-		axc = self.fig.add_axes([colClusterBarX, colClusterBarY, colClusterBarW, colClusterBarH])  # axes for column side colorbar
-		dc = numpy.array(numpy.arange(len(leafIndex2)), dtype=int)
-		dc.shape = (1,len(leafIndex2)) 
-		axc.matshow(dc, aspect='auto', origin='lower', cmap=sampleColourMap)
-		axc.set_xticks([]) 
-		axc.set_yticks([])
+		ind2 = ind2[leafIndex2] 
+
+		if self.bShowTopDendrogram:
+			axc = self.fig.add_axes([colClusterBarX, colClusterBarY, colClusterBarW, colClusterBarH])  # axes for column side colorbar
+			dc = numpy.array(numpy.arange(len(leafIndex2)), dtype=int)
+			dc.shape = (1,len(leafIndex2)) 
+			axc.matshow(dc, aspect='auto', origin='lower', cmap=sampleColourMap)
+			axc.set_xticks([]) 
+			axc.set_yticks([])
 
 		# plot row clustering bars
 		matrix = matrix[leafIndex1,:]
-		ind1 = ind1[leafIndex1,:]
-
-		axr = self.fig.add_axes([rowClusterBarX, rowClusterBarY, rowClusterBarW, rowClusterBarH]) 
-		dr = numpy.array(ind1, dtype=int)
-		dr.shape = (len(ind1),1)
-		axr.matshow(dr, aspect='auto', origin='lower', cmap=self.discreteColourMap)
-		axr.set_xticks([]) 
-		axr.set_yticks([])
+		ind1 = ind1[leafIndex1]
+
+		if self.bShowLeftDendrogram:
+			axr = self.fig.add_axes([rowClusterBarX, rowClusterBarY, rowClusterBarW, rowClusterBarH]) 
+			dr = numpy.array(ind1, dtype=int)
+			dr.shape = (len(ind1),1)
+			axr.matshow(dr, aspect='auto', origin='lower', cmap=self.discreteColourMap)
+			axr.set_xticks([]) 
+			axr.set_yticks([])
 
 		# determine scale for colour map
 		minValue = 1e6
@@ -372,6 +380,7 @@ def configure(self, profile, statsResults):
 		configDlg = ConfigureDialog(Ui_HeatmapPlotDialog)
 
 		configDlg.ui.cboFieldToPlot.setCurrentIndex(configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
+		configDlg.ui.chkPlotOnlyActiveFeatures.setChecked(self.bPlotOnlyActiveFeatures)
 
 		configDlg.ui.spinFigWidth.setValue(self.figWidth)
 		configDlg.ui.spinFigHeight.setValue(self.figHeight)
@@ -401,6 +410,7 @@ def configure(self, profile, statsResults):
 
 		if configDlg.exec_() == QtGui.QDialog.Accepted:
 			self.fieldToPlot = str(configDlg.ui.cboFieldToPlot.currentText())
+			self.bPlotOnlyActiveFeatures = configDlg.ui.chkPlotOnlyActiveFeatures.isChecked()
 
 			self.figWidth = configDlg.ui.spinFigWidth.value()
 			self.figHeight = configDlg.ui.spinFigHeight.value()
@@ -430,6 +440,7 @@ def configure(self, profile, statsResults):
 			self.dendrogramHeight = configDlg.ui.spinDendrogramHeight.value()
 
 			self.settings.setValue('group: ' + self.name + '/field to plot', self.fieldToPlot)
+			self.settings.setValue('group: ' + self.name + '/plot only active features', self.bPlotOnlyActiveFeatures)
 			self.settings.setValue('group: ' + self.name + '/width', self.figWidth)
 			self.settings.setValue('group: ' + self.name + '/height', self.figHeight)
 			self.settings.setValue('group: ' + self.name + '/dendrogram method', self.dendrogramMethod)

stamp/plugins/groups/plots/configGUI/HeatmapPlot.ui

@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>260</width>
-    <height>432</height>
+    <height>455</height>
    </rect>
   </property>
   <property name="sizePolicy">
@@ -58,6 +58,13 @@
      </item>
     </layout>
    </item>
+   <item>
+    <widget class="QCheckBox" name="chkPlotOnlyActiveFeatures">
+     <property name="text">
+      <string>Plot only active features</string>
+     </property>
+    </widget>
+   </item>
    <item>
     <widget class="QGroupBox" name="groupBox_3">
      <property name="title">

stamp/plugins/groups/plots/configGUI/HeatmapPlotUI.py

@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'HeatmapPlot.ui'
 #
-# Created: Wed Oct 16 11:32:12 2013
+# Created: Sat Jul 26 11:13:18 2014
 #      by: PyQt4 UI code generator 4.9.6
 #
 # WARNING! All changes made in this file will be lost!
@@ -26,14 +26,14 @@ def _translate(context, text, disambig):
 class Ui_HeatmapPlotDialog(object):
     def setupUi(self, HeatmapPlotDialog):
         HeatmapPlotDialog.setObjectName(_fromUtf8("HeatmapPlotDialog"))
-        HeatmapPlotDialog.resize(260, 432)
+        HeatmapPlotDialog.resize(260, 455)
         sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(HeatmapPlotDialog.sizePolicy().hasHeightForWidth())
         HeatmapPlotDialog.setSizePolicy(sizePolicy)
         icon = QtGui.QIcon()
-        icon.addPixmap(QtGui.QPixmap(_fromUtf8(":/icons/icons/programIcon.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
+        icon.addPixmap(QtGui.QPixmap(_fromUtf8("../../../../../icons/programIcon.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
         HeatmapPlotDialog.setWindowIcon(icon)
         self.verticalLayout_3 = QtGui.QVBoxLayout(HeatmapPlotDialog)
         self.verticalLayout_3.setObjectName(_fromUtf8("verticalLayout_3"))
@@ -53,6 +53,9 @@ def setupUi(self, HeatmapPlotDialog):
         self.cboFieldToPlot.addItem(_fromUtf8(""))
         self.horizontalLayout_6.addWidget(self.cboFieldToPlot)
         self.verticalLayout_3.addLayout(self.horizontalLayout_6)
+        self.chkPlotOnlyActiveFeatures = QtGui.QCheckBox(HeatmapPlotDialog)
+        self.chkPlotOnlyActiveFeatures.setObjectName(_fromUtf8("chkPlotOnlyActiveFeatures"))
+        self.verticalLayout_3.addWidget(self.chkPlotOnlyActiveFeatures)
         self.groupBox_3 = QtGui.QGroupBox(HeatmapPlotDialog)
         self.groupBox_3.setObjectName(_fromUtf8("groupBox_3"))
         self.verticalLayout = QtGui.QVBoxLayout(self.groupBox_3)
@@ -269,6 +272,7 @@ def retranslateUi(self, HeatmapPlotDialog):
         self.label.setText(_translate("HeatmapPlotDialog", "Field to plot:", None))
         self.cboFieldToPlot.setItemText(0, _translate("HeatmapPlotDialog", "Number of sequences", None))
         self.cboFieldToPlot.setItemText(1, _translate("HeatmapPlotDialog", "Proportion of sequences (%)", None))
+        self.chkPlotOnlyActiveFeatures.setText(_translate("HeatmapPlotDialog", "Plot only active features", None))
         self.groupBox_3.setTitle(_translate("HeatmapPlotDialog", "Figure size", None))
         self.lblFigureWidth.setText(_translate("HeatmapPlotDialog", "Width:", None))
         self.lblFigureHeight.setText(_translate("HeatmapPlotDialog", "Height:", None))