def normalize_pathways(self):
"""
Runs the pathway analysis options.
"""
if self.input_builder:
self.pw_analyzer= PathwayAnalyzer(self.biodb_selector, self.input_builder)
#####
if self.pw_length:
print "normalizing by sequence length"
self.pw_analyzer.normalize_by_pathway('sequence_length')
if self.pw_sequence:
print "normalizing by the number of proteins/enzymes in the pathway"
self.pw_analyzer.normalize_by_pathway('n_protein')
if self.pw_minpath:
print "normalizing by the minpath algorithm"
self.pw_analyzer.normalize_by_algorithm('minpath')
if self.pw_key_enzyme >= 0:
key_enzyme_type= self.pw_key_enzyme
if key_enzyme_type == 0 or key_enzyme_type == 1:
self.pw_analyzer.filter_pathways_by_key_leaf_features(key_enzyme_type)
### key_enzyme_type 2 is disabled in the commandline version.
elif key_enzyme_type == 3:
assert self.n_association >= 0, "You have not set the criteria for the numnber of pathway associations."
print "Running the pathway association check. Please wait..."
self.pw_analyzer.filter_pathways_by_key_leaf_features(3, self.n_association)
self.data_frame= self.input_builder.assembler.to_data_frame()
#########################################
print "OK"
else:
print "Select an input file first"
def onPathwayAnalysis(self, e):
"""
GUI: Displays a dialog window to adjust pathway analysis settings.
"""
if self.input_builder:
self.pw_controller= PathwayController(self.biodb_selector, self.input_builder)
pw_panel= self.pw_controller.view.pnl
pw_length_query= pw_panel.cbPwLength.IsChecked()
pw_sequence_query= pw_panel.cbPwSeq.IsChecked()
pw_minpath_query= pw_panel.cbMinPath.IsChecked()
status_text = ""
if pw_length_query:
status_text+= "Normalizing pathway data by sequence length! "
if pw_sequence_query:
status_text+= "Normalizing pathway data by the total number \
of proteins/enzymes in the pathways! "
if pw_minpath_query:
status_text+= "Normalizing pathway data by the minpath algorithm! "
status_text+= "Running the pathway association check! Please wait..."
self.view.statusBar.SetStatusText("PACFM: %s"%status_text)
response= self.pw_controller.view.ShowModal()
if response == wx.ID_OK:
self.pw_analyzer= PathwayAnalyzer(self.biodb_selector, self.input_builder)
if pw_length_query:
self.pw_analyzer.normalize_by_pathway('sequence_length')
if pw_sequence_query:
self.pw_analyzer.normalize_by_pathway('n_protein')
if pw_minpath_query:
self.pw_analyzer.normalize_by_algorithm('minpath')
key_enzyme_type= self.pw_controller.key_enzyme_type
if key_enzyme_type == 0 or key_enzyme_type == 1:
self.pw_analyzer.filter_pathways_by_key_leaf_features(key_enzyme_type)
elif key_enzyme_type == 3:
n_association= pw_panel.spinAss.GetValue()
self.pw_analyzer.filter_pathways_by_key_leaf_features(3, n_association)
self.normalized= True
self.pnlNormData= GridPanel(self.view.nb.pnlNormData, -1)
data_frame= self.input_builder.assembler.to_data_frame()
self.pnlNormData.grid.UpdateTable(data_frame)
self.normalized= True
self.view.nb.ChangeSelection(0)
self.view.nb.analysisBook.ChangeSelection(1)
#### find replacement for the below lines
# There should be a simpler pnl.Refresh() method!
sizer= wx.BoxSizer()
sizer.Add(self.pnlNormData, 1, wx.EXPAND)
self.view.nb.pnlNormData.SetSizer(sizer)
self.view.nb.pnlNormData.Layout()
#########################################
self.enable_normalized_controls(True)
print "OK"
status_text= "Pathway analyses have been successfully performed!"
self.view.statusBar.SetStatusText("PACFM: %s"%status_text)
else:
print "Cancel"
## included pathways are handled in the pathway_controller module
else:
print "Select a file first"
class PacfmCL(PacfmBase):
"""
Commandline interface for PACFM.
"""
def __init__(self, pw_length=False, pw_sequence=False, pw_minpath=False, pw_key_enzyme=-1, n_association=1000, input_file_path="", output_figure_path="pacfm.png", output_table_path="pacfm.tsv", output_type=0, info_types=[], abbreviations_path= "abbreviations.txt", links_path= "links.txt", key_enzymes_path="key_enzymes.txt", calculation_type= "sum", db_name="kegg_orthology", colorbar_title= "Relative abundance"):
PacfmBase.__init__(self, normalized= False, pw_length= pw_length, pw_sequence= pw_sequence, pw_minpath= pw_minpath, pw_key_enzyme= pw_key_enzyme, n_association= n_association, input_file_path= input_file_path, output_figure_path= output_figure_path, output_table_path= output_table_path, output_type= output_type, info_types= info_types, abbreviations_path= abbreviations_path, links_path= links_path, key_enzymes_path=key_enzymes_path, calculation_type= calculation_type, db_name= db_name, colorbar_title= colorbar_title )
def init_variables(self, **kwargs):
"""
overriden method
"""
###
self.pw_length= kwargs['pw_length']
self.pw_sequence= kwargs['pw_sequence']
self.pw_minpath= kwargs['pw_minpath']
self.pw_key_enzyme= kwargs['pw_key_enzyme']
###
self.n_association= kwargs['n_association']
###
self.input_file_path= kwargs['input_file_path']
self.output_figure_path= kwargs['output_figure_path']
self.output_table_path= kwargs['output_table_path']
###
self.output_type= kwargs['output_type']
###
self.info_types= kwargs['info_types']
self.abbreviations_path= kwargs['abbreviations_path']
self.links_path= kwargs['links_path']
self.key_enzymes_path= kwargs['key_enzymes_path']
###
self.calculation_type= kwargs['calculation_type']
self.db_name= kwargs['db_name']
self.colorbar_title= kwargs['colorbar_title']
### COMMANDLINE SPECIFIC ###
def init_project(self):
self.biodb_selector= Selector(self.db_name)
self.input_builder= InputBuilder(biodb_selector= self.biodb_selector, fam_path= self.input_file_path, calculation_type= self.calculation_type)
def normalize_pathways(self):
"""
Runs the pathway analysis options.
"""
if self.input_builder:
self.pw_analyzer= PathwayAnalyzer(self.biodb_selector, self.input_builder)
#####
if self.pw_length:
print "normalizing by sequence length"
self.pw_analyzer.normalize_by_pathway('sequence_length')
if self.pw_sequence:
print "normalizing by the number of proteins/enzymes in the pathway"
self.pw_analyzer.normalize_by_pathway('n_protein')
if self.pw_minpath:
print "normalizing by the minpath algorithm"
self.pw_analyzer.normalize_by_algorithm('minpath')
if self.pw_key_enzyme >= 0:
key_enzyme_type= self.pw_key_enzyme
if key_enzyme_type == 0 or key_enzyme_type == 1:
self.pw_analyzer.filter_pathways_by_key_leaf_features(key_enzyme_type)
### key_enzyme_type 2 is disabled in the commandline version.
elif key_enzyme_type == 3:
assert self.n_association >= 0, "You have not set the criteria for the numnber of pathway associations."
print "Running the pathway association check. Please wait..."
self.pw_analyzer.filter_pathways_by_key_leaf_features(3, self.n_association)
self.data_frame= self.input_builder.assembler.to_data_frame()
#########################################
print "OK"
else:
print "Select an input file first"
def plot_circos(self):
"""
Draws the final plot!
"""
if self.output_type == 0 or self.output_type == 2:
h= HighlightContainer()
h.load()
l=LinkContainer()
l.load()
p=PlotContainer()
p.load()
for ide in self.input_builder.assembler.ideograms:
p.get_by_index(ide.level-1).min_value= ide.get_min_value()
p.get_by_index(ide.level-1).max_value= ide.get_max_value()
self.input_builder.build_circos_inputs_and_run(plots= p, links= l, highlights= h)
d= Drawer(l, p, self.colorbar_title)
self.result_image= d.get_output_image()
### info ###
def save_abbreviations(self):
if not self.normalized:
ideograms= self.input_builder.assembler.ideograms
else:
ideograms= self.pw_analyzer.ideograms
for ide in ideograms:
if ide.level not in self.level_abbreviations:
self.level_abbreviations[str(ide.level)]= ide.abbreviations
with open(self.abbreviations_path, 'w') as outfile:
for level in xrange(1,4):
line1= "##### LEVEL %s #####\n" %level
outfile.write(line1)
for k, v in self.level_abbreviations[str(level)].iteritems():
line2= "%s: %s\n" %(k,v)
outfile.write(line2)
def save_key_enzyme_info(self):
"""
Saves the key enzymes into a file."
"""
if not self.normalized:
ide= self.input_builder.assembler.ideograms[-1]
else:
ide= self.pw_analyzer.ideograms[-1]
for chrom in ide.chromosomes:
self.key_enzymes[chrom.name]= [f.name for f in chrom.get_non_null_features()]
with open(self.key_enzymes_path, 'w') as outfile:
for k, v in self.key_enzymes.iteritems():
line= "%s: %s\n" %(k, ', '.join(v))
outfile.write(line)
def save_link_info(self):
"""
Saves the pathway assoication info into a file.
"""
if not self.normalized:
ide= self.input_builder.assembler.ideograms[-1]
else:
ide= self.pw_analyzer.ideograms[-1]
for id, link_coordinate in ide.link_coordinates.iteritems():
feature= self.biodb_selector.getFeatureByID(id)
pws= [coor.get_name_by_level(ide.level) for coor in link_coordinate.coordinates]
self.enzyme_pathway_link[feature.name] = pws
with open(self.links_path, 'w') as outfile:
for k, v in self.enzyme_pathway_link.iteritems():
line= "%s: %s\n" %(k, ', '.join(v))
outfile.write(line)
def save_info(self):
"""
Saves selected info types into files.
"""
if "abbreviations" in self.info_types:
self.save_abbreviations()
if "links" in self.info_types:
self.save_link_info()
if "key_enzymes" in self.info_types:
self.save_key_enzyme_info()
### info ###
### output ###
def save_data(self):
self.data_frame.to_csv(self.output_table_path, sep= "\t", index_label="Index")
def save_plot(self):
self.result_image.save(self.output_figure_path)
self.result_image.close()
def save_output(self):
if self.output_type == 0:
self.save_plot()
elif self.output_type == 1:
self.save_data()
elif self.output_type == 2:
self.save_plot()
self.save_data()
class PacfmGUI(PacfmBase):
"""
GUI class
"""
def __init__(self, wx_app= None, normalized=False, db_name="kegg_orthology", calculation_type= "sum", colorbar_title= "Relative abundance"):
PacfmBase.__init__(self, wx_app= wx_app, normalized= normalized, db_name= db_name, calculation_type= calculation_type, colorbar_title= colorbar_title)
self.view= MainView(None)
self.init_controls()
### events
self.bind_events()
### final
self.view.Show()
def init_variables(self, **kwargs):
"""
overriden method
"""
self.app = kwargs['wx_app']
self.normalized= kwargs['normalized']
self.calculation_type= kwargs["calculation_type"]
self.db_name= kwargs['db_name']
self.colorbar_title= kwargs['colorbar_title']
self.biodb_selector= None
### GUI ###
def bind_events(self):
"""
GUI: Binds events to be triggered in gui.
"""
self.view.Bind(wx.EVT_TOOL, self.onNewProject, id= self.view.newID)
self.view.Bind(wx.EVT_TOOL, self.onPathwayAnalysis, id= self.view.pathwayID)
self.view.Bind(wx.EVT_TOOL, self.onCircosPlot, id=self.view.circosID)
self.view.Bind(wx.EVT_TOOL, self.onRestart, id=self.view.homeID)
self.view.Bind(wx.EVT_CLOSE, self.onExit)
## menubar events
self.view.Bind(wx.EVT_MENU, self.onNewProject, self.view.fItemNew )
self.view.Bind(wx.EVT_MENU, self.onSaveRawData, self.view.sRawData)
self.view.Bind(wx.EVT_MENU, self.onSaveRawPlot, self.view.sRawPlot)
self.view.Bind(wx.EVT_MENU, self.onSaveNormData, self.view.sNormData)
self.view.Bind(wx.EVT_MENU, self.onSaveNormPlot, self.view.sNormPlot)
self.view.Bind(wx.EVT_MENU, self.onPathwayAbbreviations, self.view.pItemAbbr)
self.view.Bind(wx.EVT_MENU, self.onEnzymeAssociations, self.view.pItemAss)
self.view.Bind(wx.EVT_MENU, self.onKeyEnzymes, self.view.pItemKey)
def enable_toolbar_controls(self, enabled=True):
#---- TOOLBAR ----#
self.view.tb.EnableTool(self.view.pathwayID, enabled)
self.view.tb.EnableTool(self.view.homeID, enabled)
self.view.tb.EnableTool(self.view.circosID, enabled)
def enable_menubar_controls(self, enabled= True):
#---- File Menu ----#
self.view.fItemSave.Enable(enabled)
self.view.pItemAbbr.Enable(enabled)
self.view.pItemAss.Enable(enabled)
self.view.pItemKey.Enable(enabled)
def enable_controls(self, enabled= True):
self.enable_toolbar_controls(enabled)
self.enable_menubar_controls(enabled)
def enable_normalized_controls(self, enabled= True):
self.view.sNormData.Enable(enabled)
self.view.sNormPlot.Enable(enabled)
def init_controls(self):
self.enable_controls(False)
def onExit(self, e):
"""
GUI:Forcefully closes the gui.
"""
self.view.Destroy()
self.app.ExitMainLoop()
wx.WakeUpMainThread()
def onRestart(self, e):
"""
Restarts the default settings.
"""
self.loadNewProject()
def onPathwayAbbreviations(self, e):
"""
Shows the long and abbreviated forms of pathway names as shown in the figure.
"""
dlg= AbbrDialog(self.view, self.get_abbreviations())
dlg.ShowModal()
e.Skip()
def onEnzymeAssociations(self, e):
"""
Shows the pathways which each enzyme is associated with.
"""
dlg= HelpDialog(self.view, self.get_link_info(), "Enzyme Associations")
dlg.ShowModal()
def onKeyEnzymes(self, e):
"""
Shows the key enzymes of each pathway.
"""
dlg= HelpDialog(self.view, self.get_key_enzyme_info(), "Key enzymes of pathways")
dlg.ShowModal()
def get_abbreviations(self):
"""
Returns the abbreviations attribute of the ideograms \
placed at individiual hierarchy level.
"""
if not self.normalized:
ideograms= self.input_builder.assembler.ideograms
else:
ideograms= self.pw_analyzer.ideograms
for ide in ideograms:
if ide.level not in self.level_abbreviations:
self.level_abbreviations[str(ide.level)]= ide.abbreviations
return self.level_abbreviations
def get_key_enzyme_info(self):
"""
Returns the key enzymes of individual pathways as defined by the users.
"""
if not self.normalized:
ide= self.input_builder.assembler.ideograms[-1]
else:
ide= self.pw_analyzer.ideograms[-1]
for chrom in ide.chromosomes:
self.key_enzymes[chrom.name]= [f.name for f in chrom.get_non_null_features()]
return self.key_enzymes
def get_link_info(self):
"""
Returns the pathway pairs that individual enzyme is linked by.
"""
if not self.normalized:
ide= self.input_builder.assembler.ideograms[-1]
else:
ide= self.pw_analyzer.ideograms[-1]
for id, link_coordinate in ide.link_coordinates.iteritems():
feature= self.biodb_selector.getFeatureByID(id)
pws= [coor.get_name_by_level(ide.level) for coor in link_coordinate.coordinates]
self.enzyme_pathway_link[feature.name] = pws
return self.enzyme_pathway_link
def save_table(self, table, file_path):
"""
GUI: Saves the data inside a wx table.
"""
fOut= open(file_path,"w")
n_cols= table.GetColsCount()
n_rows= table.GetRowsCount()
col_names= [table.GetColLabelValue(i) for i in range(n_cols)]
header= "\t".join(col_names) + "\n"
fOut.write(header)
for j in range(n_rows):
row= []
for i in range(n_cols):
value= table.GetValue(j, i)
row.append("%s" %value)
row_line= "\t".join(row) +"\n"
fOut.write(row_line)
def get_save_plot_dialog(self):
"""
GUI: Displays a dialog window to save figures in an appropriate image format.
"""
wildcard = "PNG (*.png)|*.png|" \
"JPG (*.jpeg)|*.jpeg"
dlg = wx.FileDialog(
self.view, message="Save file as ...", defaultDir=os.getcwd(),
defaultFile="my_plot", wildcard=wildcard, style=wx.SAVE
)
return dlg
def get_save_data_dialog(self):
"""
GUI: Displays a dialog window to save data in an appropriate image format.
"""
wildcard = "Tab separated text file (*.tsv)|*.tsv"
dlg = wx.FileDialog(
self.view, message="Save file as ...", defaultDir=os.getcwd(),
defaultFile="my_data", wildcard=wildcard, style=wx.SAVE
)
return dlg
def onSaveRawData(self, e):
"""
GUI: Saves the raw data to a file.
"""
dlg= self.get_save_data_dialog()
if dlg.ShowModal() == wx.ID_OK:
file_path= dlg.GetPath()
table= self.pnlRawData.grid.GetTable()
self.save_table(table, file_path)
def onSaveNormData(self, e):
"""
Saves the normalized data to a file.
"""
dlg= self.get_save_data_dialog()
if dlg.ShowModal() == wx.ID_OK:
file_path= dlg.GetPath()
table= self.pnlNormData.grid.GetTable()
self.save_table(table, file_path)
def save_plot(self, plot_panel):
"""
GUI: Saves the PACFM plot inside a wx panel.
"""
dlg= self.get_save_plot_dialog()
if dlg.ShowModal() == wx.ID_OK:
file_path= dlg.GetPath()
if file_path.lower().endswith(".png"):
plot_panel.wxImage.SaveFile(file_path, wx.BITMAP_TYPE_PNG)
elif file_path.lower().endswith(".jpg") or file_path.lower().endswith(".jpeg"):
plot_panel.wxImage.SaveFile(file_path, wx.BITMAP_TYPE_JPEG)
else:
print file_path
def onSaveRawPlot(self, e):
"""
Saves the raw data plot to a file.
"""
self.save_plot(self.pltRawData)
def onSaveNormPlot(self, e):
"""
Saves the raw data plot to a file.
"""
self.save_plot(self.pltNormData)
def onNewProject(self, e):
"""
GUI: Displays a dialog window to start a new project.
"""
dlg= NewProjectDialog(None)
if dlg.ShowModal() == wx.ID_OK:
self.file_path= dlg.txtBrowse.GetValue()
if dlg.rbAbundance or dlg.rbRelative:
self.calculation_type = "sum"
self.colorbar_title= dlg.input_type
elif dlg.rbFoldChange:
self.calculation_type= "average"
self.project_name= dlg.txtProjectName.GetValue()
self.view.statusBar.SetStatusText("PACFM: Loading a new project... \
Please wait!")
self.db_name= dlg.cbDB.GetStringSelection()
self.loadNewProject()
self.view.statusBar.SetStatusText("PACFM: A new project \
has been successfully loaded!")
else:
pass
# self.view.statusBar.SetStatusText("PACFM: Start a new project!")
#wildcard = "Tab-separated text file (*.tsv)|*.tsv|" \
# "(*.txt)|*.txt"
#dlg= wx.FileDialog(self.view, message="Choose a tab-separated text \
# file (*.tsv |*.txt)",
# defaultFile="",
# wildcard= wildcard,
# style=wx.FD_OPEN | wx.FD_CHANGE_DIR
# )
def onOpenProject(self, e):
"""
GUI: Displays a dialog window to start an existing pacfm \
project with the .pac extension.
"""
wildcard = "PACFM files (*.pac)|*.pac"
dlg= wx.FileDialog(self.view, message="Choose a file",
defaultFile="",
wildcard=wildcard,
style=wx.OPEN | wx.CHANGE_DIR
)
e.Skip()
def loadNewProject(self):
"""
Resets the variables to default settings and loads the new project into PACFM.
"""
if self.biodb_selector:
# check if this is enough to switch from a database to another.
del self.biodb_selector
self.biodb_selector= Selector(self.db_name)
self.input_builder= InputBuilder(self.biodb_selector, self.file_path, calculation_type= self.calculation_type)
self.pnlRawData= GridPanel(self.view.nb.pnlRawData, -1)
data_frame= self.input_builder.assembler.to_data_frame()
self.pnlRawData.grid.UpdateTable(data_frame)
#### find replacement for the below lines
# There should be a simpler pnl.Refresh() method!
sizer= wx.BoxSizer()
sizer.Add(self.pnlRawData, 1, wx.EXPAND)
self.view.nb.pnlRawData.SetSizer(sizer)
self.view.nb.pnlRawData.Layout()
#########################################
self.view.nb.ChangeSelection(0)
self.view.nb.analysisBook.ChangeSelection(0)
self.normalized= False
self.enable_controls(True)
self.enable_normalized_controls(False)
def onPathwayAnalysis(self, e):
"""
GUI: Displays a dialog window to adjust pathway analysis settings.
"""
if self.input_builder:
self.pw_controller= PathwayController(self.biodb_selector, self.input_builder)
pw_panel= self.pw_controller.view.pnl
pw_length_query= pw_panel.cbPwLength.IsChecked()
pw_sequence_query= pw_panel.cbPwSeq.IsChecked()
pw_minpath_query= pw_panel.cbMinPath.IsChecked()
status_text = ""
if pw_length_query:
status_text+= "Normalizing pathway data by sequence length! "
if pw_sequence_query:
status_text+= "Normalizing pathway data by the total number \
of proteins/enzymes in the pathways! "
if pw_minpath_query:
status_text+= "Normalizing pathway data by the minpath algorithm! "
status_text+= "Running the pathway association check! Please wait..."
self.view.statusBar.SetStatusText("PACFM: %s"%status_text)
response= self.pw_controller.view.ShowModal()
if response == wx.ID_OK:
self.pw_analyzer= PathwayAnalyzer(self.biodb_selector, self.input_builder)
if pw_length_query:
self.pw_analyzer.normalize_by_pathway('sequence_length')
if pw_sequence_query:
self.pw_analyzer.normalize_by_pathway('n_protein')
if pw_minpath_query:
self.pw_analyzer.normalize_by_algorithm('minpath')
key_enzyme_type= self.pw_controller.key_enzyme_type
if key_enzyme_type == 0 or key_enzyme_type == 1:
self.pw_analyzer.filter_pathways_by_key_leaf_features(key_enzyme_type)
elif key_enzyme_type == 3:
n_association= pw_panel.spinAss.GetValue()
self.pw_analyzer.filter_pathways_by_key_leaf_features(3, n_association)
self.normalized= True
self.pnlNormData= GridPanel(self.view.nb.pnlNormData, -1)
data_frame= self.input_builder.assembler.to_data_frame()
self.pnlNormData.grid.UpdateTable(data_frame)
self.normalized= True
self.view.nb.ChangeSelection(0)
self.view.nb.analysisBook.ChangeSelection(1)
#### find replacement for the below lines
# There should be a simpler pnl.Refresh() method!
sizer= wx.BoxSizer()
sizer.Add(self.pnlNormData, 1, wx.EXPAND)
self.view.nb.pnlNormData.SetSizer(sizer)
self.view.nb.pnlNormData.Layout()
#########################################
self.enable_normalized_controls(True)
print "OK"
status_text= "Pathway analyses have been successfully performed!"
self.view.statusBar.SetStatusText("PACFM: %s"%status_text)
else:
print "Cancel"
## included pathways are handled in the pathway_controller module
else:
print "Select a file first"
def onCircosPlot(self, e):
"""
GUI: Runs CIRCOS and displays a modified version of the plot in PACFM.
"""
hc= HighlightContainer()
hc.load()
l=LinkContainer()
l.load()
p=PlotContainer()
p.load()
for ide in self.input_builder.assembler.ideograms:
p.get_by_index(ide.level-1).min_value= ide.get_min_value()
p.get_by_index(ide.level-1).max_value= ide.get_max_value()
self.circos_controller = CircosController(self.biodb_selector, p, l, hc)
if self.normalized:
self.circos_controller.view.plotType.rbNorm.SetValue(1)
else:
self.circos_controller.view.plotType.rbRaw.SetValue(1)
status_text= "Drawing the plot. Please wait..."
self.view.statusBar.SetStatusText("PACFM: %s"%status_text)
response= self.circos_controller.view.ShowModal()
if response == wx.ID_OK:
plots = self.circos_controller.view.plotType.plots
links= self.circos_controller.view.links.links
### filter links that are not found in the dataset
#print self.input_builder.assembler.ideograms[l.level-1].names
for name in links.names:
if name not in self.input_builder.assembler.ideograms[l.level-1].names:
links.remove(name)
highlights= self.circos_controller.view.highlights.highlights
self.input_builder.build_circos_inputs_and_run(plots= plots,
links= links, highlights= highlights)
d= Drawer(links, plots, self.colorbar_title)
result_image= d.get_output_image()
wx_image= PilImageToWxImage(result_image)
self.view.nb.ChangeSelection(1)
if not self.normalized:
self.pltRawData= CircosPanel(self.view.nb.pltRawData, wx_image)
# There should be a simpler pnl.Refresh() method!
self.view.nb.circosBook.ChangeSelection(0)
sizer= wx.BoxSizer()
sizer.Add(self.pltRawData, 1, wx.EXPAND)
#
self.view.nb.pltRawData.SetSizer(sizer)
self.view.nb.pltRawData.Layout()
else:
self.pltNormData= CircosPanel(self.view.nb.pltNormData, wx_image)
# There should be a simpler pnl.Refresh() method!
self.view.nb.circosBook.ChangeSelection(1)
sizer= wx.BoxSizer()
sizer.Add(self.pltNormData, 1, wx.EXPAND)
self.view.nb.pltNormData.SetSizer(sizer)
self.view.nb.pltNormData.Layout()
self.circos_controller.view.Destroy()
self.normalized= self.circos_controller.view.plotType.rbNorm.GetValue()
status_text= "The PACFM plot has been successfully drawn!"
self.view.statusBar.SetStatusText("PACFM: %s"%status_text)
