v2.1.2: enhancements and minor fixes to plots

examples/CoalSeamGas/coal.metadata.single_column_test.tsv

@@ -0,0 +1,45 @@
+Sample Id
+573857
+573852
+573861
+573859
+573862
+573860
+573855
+573858
+619007
+619006
+573863
+573864
+573865
+573866
+573867
+573868
+573869
+573870
+573871
+573880
+573882
+573877
+573878
+573879
+573886
+573887
+573874
+573875
+573876
+573890
+573891
+573888
+573889
+573895
+573898
+573899
+573900
+573892
+573901
+573893
+573894
+573896
+573897
+573902

stamp/STAMP.py

@@ -23,8 +23,8 @@
 __copyright__ = 'Copyright 2013'
 __credits__ = ['Donovan Parks']
 __license__ = 'GPL3'
-__version__ = '2.1.1'
-__date__ = 'June 7, 2015'
+__version__ = '2.1.2'
+__date__ = 'June 15, 2015'
 __maintainer__ = 'Donovan Parks'
 __email__ = '[email protected]'
 __status__ = 'Development'
@@ -790,7 +790,7 @@ def loadProfile(self):
 			self.ui.cboProfileLevel.setCurrentIndex(0)
 
 			# setup group legend
-			if self.metadata != None:
+			if self.metadata != None and len(self.metadata.getFeatures()) != 0:
 				self.groupLegendDlg.initLegend(self.profileTree, self.metadata, self.metadata.getFeatures()[0])
 				self.preferences['Group colours'] = self.groupLegendDlg.groupColourDict
 

stamp/plugins/groups/plots/ExtendedErrorBar.py

@@ -134,7 +134,8 @@ def plot(self, profile, statsResults):
 
 		if self.bShowCorrectedPvalues:
 			pValueLabels = statsResults.getColumnAsStr('pValuesCorrected')
-			pValueTitle += ' (corrected)'
+			if statsResults.multCompCorrection.method != 'No correction':
+				pValueTitle += ' (corrected)'
 		else:
 			pValueLabels = statsResults.getColumnAsStr('pValues')
 
@@ -369,6 +370,9 @@ def plot(self, profile, statsResults):
 				a.tick1On=False
 				a.tick2On=False
 
+			for loc, spine in axRight.spines.iteritems():
+				spine.set_color('none') 
+
 		# *** Legend
 		if self.legendPos != -1:
 			legend1 = Rectangle((0, 0), 1, 1, fc=group1Colour)

stamp/plugins/groups/plots/HeatmapPlot.py

@@ -220,10 +220,10 @@ def plot(self, profile, statsResults):
 				longestColLabel = colHeaders[i]
 
 		# *** Check sorting method and adjust dendrogram parameters appropriately
-		if self.sortRowMethod == 'Alphabetical order':
+		if self.sortRowMethod == 'Alphabetical order' or self.sortRowMethod == 'Mean abundance':
 			self.bShowRowDendrogram = False
 
-		if self.sortColMethod == 'Alphabetical order':
+		if self.sortColMethod == 'Alphabetical order' or self.sortColMethod == 'Mean abundance':
 			self.bShowColDendrogram = False
 
 		# *** Set figure size
@@ -294,17 +294,21 @@ def plot(self, profile, statsResults):
 			legendY = heatmapY + heatmapH + (1.5*yLabelBounds.height) + 0.1/self.figWidth
 
 		# plot dendrograms
-		if self.sortRowMethod != 'Alphabetical order':
+		if self.sortRowMethod == 'Alphabetical order':
+			leafIndex1 = numpy.argsort(rowHeaders)[::-1]
+		elif self.sortRowMethod == 'Mean abundance':
+			leafIndex1 = numpy.argsort(numpy.mean(matrix, axis=1))
+		else:
 			axisRowDendrogram = self.fig.add_axes([rowDendrogramX, rowDendrogramY, rowDendrogramW, rowDendrogramH], frame_on=False)
 			ind1, leafIndex1 = self.plotDendrogram(matrix, axisRowDendrogram, self.sortRowMethod, self.clusteringRowThreshold, 'right', bPlot = self.bShowRowDendrogram)
-		else:
-			leafIndex1 = numpy.argsort(rowHeaders)[::-1]
 
-		if self.sortColMethod != 'Alphabetical order':
+		if self.sortColMethod == 'Alphabetical order':
+			leafIndex2 = numpy.argsort(colHeaders)
+		elif self.sortColMethod == 'Mean abundance':
+			leafIndex2 = numpy.argsort(numpy.mean(matrix, axis=0))
+		else:
 			axisColDendrogram = self.fig.add_axes([colDendrogramX, colDendrogramY, colDendrogramW, colDendrogramH], frame_on=False)
 			ind2, leafIndex2 = self.plotDendrogram(matrix.T, axisColDendrogram, self.sortColMethod, self.clusteringColThreshold, 'top', bPlot = self.bShowColDendrogram)
-		else:
-			leafIndex2 = numpy.argsort(colHeaders)
 
 		# *** Handle mouse events
 		xCell = []

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

@@ -280,6 +280,11 @@
             <string>Alphabetical order</string>
            </property>
           </item>
+          <item>
+           <property name="text">
+            <string>Mean abundance</string>
+           </property>
+          </item>
           <item>
            <property name="text">
             <string>Average neighbour (UPGMA)</string>

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

@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'HeatmapPlot.ui'
 #
-# Created: Fri Nov 07 10:43:39 2014
+# Created: Fri Jun 12 15:15:44 2015
 #      by: PyQt4 UI code generator 4.9.6
 #
 # WARNING! All changes made in this file will be lost!
@@ -149,6 +149,7 @@ def setupUi(self, HeatmapPlotDialog):
         self.cboRowSortMethod.addItem(_fromUtf8(""))
         self.cboRowSortMethod.addItem(_fromUtf8(""))
         self.cboRowSortMethod.addItem(_fromUtf8(""))
+        self.cboRowSortMethod.addItem(_fromUtf8(""))
         self.horizontalLayout_5.addWidget(self.cboRowSortMethod)
         self.verticalLayout_2.addLayout(self.horizontalLayout_5)
         self.horizontalLayout_2 = QtGui.QHBoxLayout()
@@ -343,11 +344,12 @@ def retranslateUi(self, HeatmapPlotDialog):
         self.groupBox.setTitle(_translate("HeatmapPlotDialog", "Sort rows", None))
         self.lblDendrogramMethod.setText(_translate("HeatmapPlotDialog", "Methods:", None))
         self.cboRowSortMethod.setItemText(0, _translate("HeatmapPlotDialog", "Alphabetical order", None))
-        self.cboRowSortMethod.setItemText(1, _translate("HeatmapPlotDialog", "Average neighbour (UPGMA)", None))
-        self.cboRowSortMethod.setItemText(2, _translate("HeatmapPlotDialog", "Centroid", None))
-        self.cboRowSortMethod.setItemText(3, _translate("HeatmapPlotDialog", "Furthest neighbour", None))
-        self.cboRowSortMethod.setItemText(4, _translate("HeatmapPlotDialog", "Nearest neighbour", None))
-        self.cboRowSortMethod.setItemText(5, _translate("HeatmapPlotDialog", "Ward", None))
+        self.cboRowSortMethod.setItemText(1, _translate("HeatmapPlotDialog", "Mean abundance", None))
+        self.cboRowSortMethod.setItemText(2, _translate("HeatmapPlotDialog", "Average neighbour (UPGMA)", None))
+        self.cboRowSortMethod.setItemText(3, _translate("HeatmapPlotDialog", "Centroid", None))
+        self.cboRowSortMethod.setItemText(4, _translate("HeatmapPlotDialog", "Furthest neighbour", None))
+        self.cboRowSortMethod.setItemText(5, _translate("HeatmapPlotDialog", "Nearest neighbour", None))
+        self.cboRowSortMethod.setItemText(6, _translate("HeatmapPlotDialog", "Ward", None))
         self.lblClusteringThreshold.setText(_translate("HeatmapPlotDialog", "Dendrogram clustering threshold:", None))
         self.chkShowRowDendrogram.setText(_translate("HeatmapPlotDialog", "Show dendrogram", None))
         self.lblDendrogramWidth.setText(_translate("HeatmapPlotDialog", "Width (inches):", None))

stamp/plugins/groups/plots/pcaPlot.py

@@ -131,7 +131,7 @@ def plot(self, profile, statsResults):
 
 		axesExpandPercentage = 0.1
 
-		border = 0.25 # inches
+		border = 0.4 # inches
 		plotSpacing = 0.15
 		xLabelOffset = 0.5
 		yLabelOffset = 0.2
@@ -416,7 +416,7 @@ def configure(self, profile, statsResults):
 			self.bShowPC1vsPC3 = configDlg.ui.chkPC1vsPC3.isChecked()
 			self.bShowPC3vsPC2 = configDlg.ui.chkPC3vsPC2.isChecked()
 
-			# legend position			
+			# legend position
 			if configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
 				self.legendPos = 2
 			elif configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:

stamp/plugins/multiGroups/plots/HeatmapPlot.py

@@ -223,10 +223,10 @@ def plot(self, profile, statsResults):
 				longestColLabel = colHeaders[i]
 
 		# *** Check sorting method and adjust dendrogram parameters appropriately
-		if self.sortRowMethod == 'Alphabetical order':
+		if self.sortRowMethod == 'Alphabetical order' or self.sortRowMethod == 'Mean abundance':
 			self.bShowRowDendrogram = False
 
-		if self.sortColMethod == 'Alphabetical order':
+		if self.sortColMethod == 'Alphabetical order' or self.sortColMethod == 'Mean abundance':
 			self.bShowColDendrogram = False
 
 		# *** Set figure size
@@ -297,17 +297,21 @@ def plot(self, profile, statsResults):
 			legendY = heatmapY + heatmapH + (1.5*yLabelBounds.height) + 0.1/self.figWidth
 
 		# plot dendrograms
-		if self.sortRowMethod != 'Alphabetical order':
+		if self.sortRowMethod == 'Alphabetical order':
+			leafIndex1 = numpy.argsort(rowHeaders)[::-1]
+		elif self.sortRowMethod == 'Mean abundance':
+			leafIndex1 = numpy.argsort(numpy.mean(matrix, axis=1))
+		else:
 			axisRowDendrogram = self.fig.add_axes([rowDendrogramX, rowDendrogramY, rowDendrogramW, rowDendrogramH], frame_on=False)
 			ind1, leafIndex1 = self.plotDendrogram(matrix, axisRowDendrogram, self.sortRowMethod, self.clusteringRowThreshold, 'right', bPlot = self.bShowRowDendrogram)
-		else:
-			leafIndex1 = numpy.argsort(rowHeaders)[::-1]
 
-		if self.sortColMethod != 'Alphabetical order':
+		if self.sortColMethod == 'Alphabetical order':
+			leafIndex2 = numpy.argsort(colHeaders)
+		elif self.sortColMethod == 'Mean abundance':
+			leafIndex2 = numpy.argsort(numpy.mean(matrix, axis=0))
+		else:
 			axisColDendrogram = self.fig.add_axes([colDendrogramX, colDendrogramY, colDendrogramW, colDendrogramH], frame_on=False)
 			ind2, leafIndex2 = self.plotDendrogram(matrix.T, axisColDendrogram, self.sortColMethod, self.clusteringColThreshold, 'top', bPlot = self.bShowColDendrogram)
-		else:
-			leafIndex2 = numpy.argsort(colHeaders)
 
 		# *** Handle mouse events
 		xCell = []

stamp/plugins/multiGroups/plots/PostHocPlot.py

@@ -390,6 +390,9 @@ def plot(self, profile, statsResults):
 			for a in axRight.yaxis.majorTicks:
 				a.tick1On=False
 				a.tick2On=False
+
+			for loc, spine in axRight.spines.iteritems():
+				spine.set_color('none') 
 
 		self.updateGeometry()
 		self.draw()

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

@@ -280,6 +280,11 @@
             <string>Alphabetical order</string>
            </property>
           </item>
+          <item>
+           <property name="text">
+            <string>Mean abundance</string>
+           </property>
+          </item>
           <item>
            <property name="text">
             <string>Average neighbour (UPGMA)</string>

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

@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'HeatmapPlot.ui'
 #
-# Created: Fri Nov 07 11:02:38 2014
+# Created: Fri Jun 12 15:14:54 2015
 #      by: PyQt4 UI code generator 4.9.6
 #
 # WARNING! All changes made in this file will be lost!
@@ -149,6 +149,7 @@ def setupUi(self, HeatmapPlotDialog):
         self.cboRowSortMethod.addItem(_fromUtf8(""))
         self.cboRowSortMethod.addItem(_fromUtf8(""))
         self.cboRowSortMethod.addItem(_fromUtf8(""))
+        self.cboRowSortMethod.addItem(_fromUtf8(""))
         self.horizontalLayout_5.addWidget(self.cboRowSortMethod)
         self.verticalLayout_2.addLayout(self.horizontalLayout_5)
         self.horizontalLayout_2 = QtGui.QHBoxLayout()
@@ -343,11 +344,12 @@ def retranslateUi(self, HeatmapPlotDialog):
         self.groupBox.setTitle(_translate("HeatmapPlotDialog", "Sort rows", None))
         self.lblDendrogramMethod.setText(_translate("HeatmapPlotDialog", "Methods:", None))
         self.cboRowSortMethod.setItemText(0, _translate("HeatmapPlotDialog", "Alphabetical order", None))
-        self.cboRowSortMethod.setItemText(1, _translate("HeatmapPlotDialog", "Average neighbour (UPGMA)", None))
-        self.cboRowSortMethod.setItemText(2, _translate("HeatmapPlotDialog", "Centroid", None))
-        self.cboRowSortMethod.setItemText(3, _translate("HeatmapPlotDialog", "Furthest neighbour", None))
-        self.cboRowSortMethod.setItemText(4, _translate("HeatmapPlotDialog", "Nearest neighbour", None))
-        self.cboRowSortMethod.setItemText(5, _translate("HeatmapPlotDialog", "Ward", None))
+        self.cboRowSortMethod.setItemText(1, _translate("HeatmapPlotDialog", "Mean abundance", None))
+        self.cboRowSortMethod.setItemText(2, _translate("HeatmapPlotDialog", "Average neighbour (UPGMA)", None))
+        self.cboRowSortMethod.setItemText(3, _translate("HeatmapPlotDialog", "Centroid", None))
+        self.cboRowSortMethod.setItemText(4, _translate("HeatmapPlotDialog", "Furthest neighbour", None))
+        self.cboRowSortMethod.setItemText(5, _translate("HeatmapPlotDialog", "Nearest neighbour", None))
+        self.cboRowSortMethod.setItemText(6, _translate("HeatmapPlotDialog", "Ward", None))
         self.lblClusteringThreshold.setText(_translate("HeatmapPlotDialog", "Dendrogram clustering threshold:", None))
         self.chkShowRowDendrogram.setText(_translate("HeatmapPlotDialog", "Show dendrogram", None))
         self.lblDendrogramWidth.setText(_translate("HeatmapPlotDialog", "Width (inches):", None))