class DataMatrixGUI(gtk.Window):
"""
2009-3-13
migrated from QCVisualize.py. now become a standalone program and
able to read data from a file and plot ...
QCVisualize.py inherits from here
2008-02-05
embed it into a bigger gnome app, add more buttons, and change the __init__()
2008-01-01
class to visualize the results from QualityControl.py
"""
def __init__(self, plot_title='', id_is_strain=1, header=None,
strain_acc_list=None, category_list=None, data_matrix=None):
"""
2008-01-10
use a paned window to wrap the scrolledwindow and the canvas
so that the relative size of canvas to the scrolledwindow could be adjusted by the user.
"""
prog = gnome.program_init('DataMatrixGUI', '0.1')
#this must be called before any initialization for gnome app
program_path = os.path.dirname(__init__.__file__)
xml = gtk.glade.XML(os.path.join(program_path, 'DataMatrixGUI.glade'))
xml.signal_autoconnect(self)
self.app1 = xml.get_widget("app1")
self.app1.connect("delete_event", gtk.main_quit)
self.app1.set_default_size(800, 1000)
self.app1.set_title(plot_title)
self.plot_title = plot_title
self.id_is_strain = id_is_strain
self.header = header
self.strain_acc_list = strain_acc_list
self.category_list = category_list
self.data_matrix = data_matrix
self.inputDataHeaders = None
self.columnTypes = None
self.columnHeaders = None
self.columnEditableFlagList = None
self.list2D = None
self.vbox1 = xml.get_widget("vbox1")
self.treeview_matrix = xml.get_widget("treeview_matrix")
# matplotlib stuff
fig = Figure(figsize=(8,8))
self.canvas = FigureCanvas(fig) # a gtk.DrawingArea
self._idClick = self.canvas.mpl_connect('button_press_event', self.onUserClickCanvas)
self.vpaned1 = xml.get_widget("vpaned1")
self.vpaned1.add2(self.canvas)
#self.vbox1.pack_start(self.canvas, True, True)
self.ax = fig.add_subplot(111)
self.treeview_matrix.connect('row-activated', self.plot_row)
toolbar = NavigationToolbar(self.canvas, self.app1)
self.vbox1.pack_start(toolbar, False, False)
self.checkbutton_label_dot = xml.get_widget('checkbutton_label_dot')
self.entry_dot_label_column = xml.get_widget('entry_dot_label_column')
self.dataLabelColumnIndexAndSeparatorList = None
self.dataLabelNumericItemIndexList = None
self.entry_x_na = xml.get_widget('entry_x_na')
self.entry_y_na = xml.get_widget('entry_y_na')
self.entry_multiply_x = xml.get_widget('entry_multiply_x')
self.entry_multiply_y = xml.get_widget('entry_multiply_y')
self.entry_add_x = xml.get_widget('entry_add_x')
self.entry_add_y = xml.get_widget('entry_add_y')
self.entry_x_error = xml.get_widget("entry_x_error")
self.entry_y_error = xml.get_widget("entry_y_error")
self.checkbutton_logX = xml.get_widget('checkbutton_logX')
self.checkbutton_logY = xml.get_widget('checkbutton_logY')
self.checkButtonPlotOnlySelected = xml.get_widget('checkButtonPlotOnlySelected')
self.entry_x_column = xml.get_widget('entry_x_column')
self.entry_y_column = xml.get_widget('entry_y_column')
self.entry_filters = xml.get_widget("entry_filters")
#self.checkbutton_histLogX = xml.get_widget('checkbutton_histLogX')
#self.checkbutton_histLogY = xml.get_widget('checkbutton_histLogY')
self.entry_hist_column = xml.get_widget('entry_hist_column')
self.entry_no_of_bins = xml.get_widget('entry_no_of_bins')
self.entry_plot_title = xml.get_widget('entry_plot_title')
self.entry_plot_title.set_text(self.plot_title)
self.filechooserdialog_save = xml.get_widget("filechooserdialog_save")
self.filechooserdialog_save.connect("delete_event", yh_gnome.subwindow_hide)
self.entry_sampling_probability = xml.get_widget("entry_sampling_probability")
self.filechooserdialog_open = xml.get_widget("filechooserdialog_open")
self.filechooserdialog_open.connect("delete_event", yh_gnome.subwindow_hide)
self.app1_appbar1 = xml.get_widget('app1_appbar1')
self.app1_appbar1.push('Status Message.') #import gnome.ui has to be executed.
self.treeview_matrix.connect('cursor-changed', self.update_no_of_selected, self.app1_appbar1)
self.app1.show_all()
self.xValuePreProcessor = None
self.yValuePreProcessor = None
self.x_error_column_index = None
self.y_error_column_index = None
self.typeName2PythonType = {
"str": str,
"string": str,
"numeric":float,
"number":float,
"double":float,
"float":float,
"integer":int,
"int":int}
#self.add_events(gdk.BUTTON_PRESS_MASK|gdk.KEY_PRESS_MASK|gdk.KEY_RELEASE_MASK)
def parseDataLabelColumns(self, inputText):
"""
2015.04.16
"""
splitP= re.compile(r'([,/|\.\-_=\?:;"\'^%$@+])')
#any single character included could be used as splitter
self.dataLabelColumnIndexAndSeparatorList = splitP.split(inputText)
self.dataLabelNumericItemIndexList = []
for i in range(len(self.dataLabelColumnIndexAndSeparatorList)):
if not splitP.match(self.dataLabelColumnIndexAndSeparatorList[i]):
#it's a column index
self.dataLabelColumnIndexAndSeparatorList[i] = int(self.dataLabelColumnIndexAndSeparatorList[i])
self.dataLabelNumericItemIndexList.append(i)
return self.dataLabelColumnIndexAndSeparatorList, self.dataLabelNumericItemIndexList
def getDataPointLabel(self, dataRow):
"""
2015.04.16
"""
dataLabelInList = copy.deepcopy(self.dataLabelColumnIndexAndSeparatorList)
for i in self.dataLabelNumericItemIndexList:
dataLabelInList[i] = str(dataRow[self.dataLabelColumnIndexAndSeparatorList[i]])
return ''.join(dataLabelInList)
def onUserClickCanvas(self, event):
"""
2016.06.07 bugfix. zero(0) generates false condition while only empty string or None should generate false.
2009-3-13
use (x_lim[1]-x_lim[0])/200. as the resolution for a dot to be called identical to a data point.
similar for the y_data
2009-3-13
deal with checkbutton_label_dot, entry_dot_label_column, entry_x_column, entry_y_column
2008-01-01
derived from on_click_row() of QualityControl.py
reaction when user clicked in the plot
"""
# get the x and y coords, flip y from top to bottom
x, y = event.x, event.y
toLabelDataPoint = self.checkbutton_label_dot.get_active()
self.parseDataLabelColumns(self.entry_dot_label_column.get_text())
x_column = int(self.entry_x_column.get_text())
y_column = int(self.entry_y_column.get_text())
x_lim = self.ax.get_xlim()
x_grain_size = abs(x_lim[1]-x_lim[0])/200.
y_lim = self.ax.get_ylim()
y_grain_size = abs(y_lim[1]-y_lim[0])/200.
if event.button==1:
if event.inaxes is not None:
sys.stderr.write("x_grain_size: %s, y_grain_size: %s\n"%(x_grain_size, y_grain_size))
sys.stderr.write("data coords: %s, %s\n"%(event.xdata, event.ydata))
if self.list2D is None:
return
for row in self.list2D:
if row[x_column] is not None and row[x_column]!="" and \
row[y_column] is not None and row[y_column]!="" : #not empty
#2016.06.07
try:
x_data = float(row[x_column])
y_data = float(row[y_column])
x = self.processDataValue(x_data, self.xValuePreProcessor)
if x is None:
continue
y = self.processDataValue(y_data, self.yValuePreProcessor)
if y is None:
continue
if abs(x-event.xdata)<x_grain_size and abs(y-event.ydata)<y_grain_size:
dataLabel = self.getDataPointLabel(row)
if toLabelDataPoint:
self.ax.text(event.xdata, event.ydata, dataLabel, size=8)
self.canvas.draw()
sys.stderr.write("%s: %s, %s: %s, raw xy=(%s, %s), scaled xy=(%s,%s), dataLabel: %s.\n"%\
(self.columnHeaders[0], row[0], self.columnHeaders[1], row[1],
row[x_column], row[y_column], x,y, dataLabel))
except:
sys.stderr.write("Column %s, %s of row (%s), could not be converted to float. skip.\n"%\
(x_column, y_column, repr(row)))
def setUserDataPreprocessingFlags(self):
"""
2014.07.25
"""
self.xValuePreProcessor = ValuePreProcessor(na = self.entry_x_na.get_text())
self.yValuePreProcessor = ValuePreProcessor(na = self.entry_y_na.get_text())
if self.entry_multiply_x.get_text():
self.xValuePreProcessor.scalar = float(self.entry_multiply_x.get_text())
if self.entry_multiply_y.get_text():
self.yValuePreProcessor.scalar = float(self.entry_multiply_y.get_text())
if self.entry_add_x.get_text():
self.xValuePreProcessor.addition = float(self.entry_add_x.get_text())
if self.entry_add_y.get_text():
self.yValuePreProcessor.addition = float(self.entry_add_y.get_text())
if self.entry_x_error.get_text():
self.xValuePreProcessor.errorColumnIndex = int(self.entry_x_error.get_text())
if self.entry_y_error.get_text():
self.yValuePreProcessor.errorColumnIndex = int(self.entry_y_error.get_text())
if self.checkbutton_logX.get_active():
self.xValuePreProcessor.logScale = True
if self.checkbutton_logY.get_active():
self.yValuePreProcessor.logScale = True
def processDataValue(self, value=None, valuePreProcessor=None):
"""
2014.07.31
"""
if valuePreProcessor.na is not None and (value==valuePreProcessor.na or \
float(value)==float(valuePreProcessor.na)):
return None
value = float(value)
if valuePreProcessor.scalar is not None:
value = value*valuePreProcessor.scalar
if valuePreProcessor.addition is not None:
value = value + valuePreProcessor.addition
return value
def decorateAxisLabel(self, label=None, valuePreProcessor=None):
"""
2014.07.31
"""
if valuePreProcessor.scalar is not None:
label = "%s*%s"%(valuePreProcessor.scalar, label)
if valuePreProcessor.addition:
label = "%s+%s"%(label, valuePreProcessor.addition)
return label
def filterDataRow(self, dataRow):
"""
2015.4.16
unfinished
"""
logicSplitP= re.compile(r'(AND|OR)')
equationSplitP = re.compile(r'>=|>|=|<|<=')
filtersText = self.entry_filters.get_text()
logicSplitP.split(filtersText)
self.dataLabelColumnIndexAndSeparatorList = splitP.split(inputText)
self.dataLabelNumericItemIndexList = []
for i in range(len(self.dataLabelColumnIndexAndSeparatorList)):
if not splitP.match(self.dataLabelColumnIndexAndSeparatorList[i]): #it's a column index
self.dataLabelColumnIndexAndSeparatorList[i] = \
int(self.dataLabelColumnIndexAndSeparatorList[i])
self.dataLabelNumericItemIndexList.append(i)
def plotXY(self, ax, canvas, liststore, plot_title='',
chosen_index_ls=[]):
"""
2015.01.28 add summary stats to title
2014.04.29 add error bars
2009-3-13
rename plot_NA_mismatch_rate to plotXY()
2008-02-05
chosen_index => chosen_index_ls
2007-12-14
"""
x_column = int(self.entry_x_column.get_text())
y_column = int(self.entry_y_column.get_text())
self.setUserDataPreprocessingFlags()
plot_title = self.entry_plot_title.get_text()
min_x = 1
min_y = 1
max_x = 0
max_y = 0
x_ls = []
x_error_ls = []
y_ls = []
y_error_ls = []
x_chosen_ls = []
x_chosen_error_ls = []
y_chosen_ls = []
y_chosen_error_ls = []
noOfValuesDiscarded = 0
chosen_index_set = set(chosen_index_ls)
for i in range(len(liststore)):
row = liststore[i]
x = row[x_column]
y = row[y_column]
if x=='' or y=='':
continue
noOfValuesDiscarded += 1
x = self.processDataValue(x, self.xValuePreProcessor)
if x is None:
continue
noOfValuesDiscarded += 1
y = self.processDataValue(y, self.yValuePreProcessor)
if y is None:
continue
noOfValuesDiscarded += 1
#self.filterDataRow()
if self.xValuePreProcessor.errorColumnIndex is not None:
x_error = row[self.xValuePreProcessor.errorColumnIndex]
else:
x_error = 0
if self.yValuePreProcessor.errorColumnIndex is not None:
y_error = row[self.yValuePreProcessor.errorColumnIndex]
else:
y_error = 0
if x<min_x:
min_x = x
if x>max_x:
max_x = x
if y<min_y:
min_y = y
if y>max_y:
max_y = y
if i in chosen_index_set:
x_chosen_ls.append(x)
y_chosen_ls.append(y)
x_chosen_error_ls.append(x_error)
y_chosen_error_ls.append(y_error)
else:
x_ls.append(x)
y_ls.append(y)
x_error_ls.append(x_error)
y_error_ls.append(y_error)
sys.stderr.write("WARNING: %s values were discarded.\n"%(noOfValuesDiscarded))
ax.clear()
if self.xValuePreProcessor.logScale:
ax.set_xscale('log')
if self.yValuePreProcessor.logScale:
ax.set_yscale('log')
#plot unselected data only if
if not self.checkButtonPlotOnlySelected.get_active():
if self.x_error_column_index is not None and self.y_error_column_index is not None:
ax.errorbar(x_ls, y_ls, xerr=x_error_ls, yerr=y_error_ls, ecolor='g', fmt='o')
else:
ax.plot(x_ls, y_ls, 'o', alpha=0.7, linewidth=0, linestyle="None")
"""
#diagonal line give a rough feeling about the notion, more NA, worse calling
diagonal_start = min(min_x, min_y)-0.1
diagonal_end = max(max_x, max_x)+0.1
ax.plot([diagonal_start, diagonal_end],[diagonal_start, diagonal_end])
"""
if x_chosen_ls and y_chosen_ls: #highlight
titleWithStats = "Highlighted data\n" + \
yh_matplotlib.constructTitleFromTwoDataSummaryStat(x_chosen_ls, y_chosen_ls)
ax.plot(x_chosen_ls, y_chosen_ls, 'o', alpha=0.6, c='r')
if self.x_error_column_index is not None and self.y_error_column_index is not None:
ax.errorbar(x_chosen_ls, y_chosen_ls, xerr=x_chosen_error_ls,
yerr=y_chosen_error_ls, ecolor='r', color='r', fmt='o')
else: #take all data
titleWithStats = yh_matplotlib.\
constructTitleFromTwoDataSummaryStat(x_ls+x_chosen_ls, y_ls+y_chosen_ls)
if plot_title:
ax.set_title("%s %s"%(plot_title, titleWithStats))
else:
ax.set_title(titleWithStats)
xlabel = "(%s)"%self.columnHeaders[x_column]
xlabel = self.decorateAxisLabel(xlabel, self.xValuePreProcessor)
ax.set_xlabel(xlabel)
ylabel = "(%s)"%self.columnHeaders[y_column]
ylabel = self.decorateAxisLabel(ylabel, self.yValuePreProcessor)
ax.set_ylabel(ylabel)
canvas.draw()
def plot_row(self, treeview, path, view_column):
if self._idClick==None:
self._idClick = self.canvas.mpl_connect('button_press_event', self.onUserClickCanvas)
self.plotXY(self.ax, self.canvas, self.liststore, self.plot_title, path)
def setupColumns(self, treeview):
"""
2009-3-13
"""
if not getattr(self, 'columnHeaders', None):
sys.stderr.write("Nothing in columns yet.\n")
return
self.liststore = gtk.ListStore(*self.columnTypes)
#self.add_columns(self.treeview_matrix)
yh_gnome.create_columns(self.treeview_matrix, self.columnHeaders,
self.columnEditableFlagList, self.liststore)
yh_gnome.fill_treeview(self.treeview_matrix, self.liststore, self.list2D, reorderable=True)
self.treeselection = self.treeview_matrix.get_selection()
def on_button_PlotXY_clicked(self, widget, data=None):
"""
2008-02-12
to update the no_of_selected rows
(have to double click a row to change a cursor if it's multiple selection)
"""
if self._idClick==None:
self._idClick = self.canvas.mpl_connect('button_press_event', self.onUserClickCanvas)
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
index_ls = []
for path in pathlist_strains1:
index_ls.append(path[0])
self.app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
self.plotXY(self.ax, self.canvas, self.liststore, self.plot_title, index_ls)
def on_button_UnSelectAll_clicked(self, widget, data=None):
"""
2015.04.16
"""
self.treeselection = self.treeview_matrix.get_selection()
self.treeselection.unselect_all()
def on_button_save_clicked(self, widget, data=None):
"""
2008-02-05
"""
self.filechooserdialog_save.show_all()
def on_button_filechooserdialog_cancel_ok_clicked(self, widget, data=None):
"""
2008-02-05
"""
self.filechooserdialog_save.hide()
def on_button_filechooserdialog_save_ok_clicked(self, widget, data=None):
"""
2008-02-12
to update the no_of_selected rows (have to double click a row to change a cursor if it's multiple selection)
2008-02-05
"""
output_fname = self.filechooserdialog_save.get_filename()
self.filechooserdialog_save.hide()
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
self.app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
if self.header and self.strain_acc_list and self.category_list and self.data_matrix:
selected_index_set = set()
for path in pathlist_strains1:
row = self.liststore[path[0]]
id = row[0]
index_in_data_matrix = row[-1]
selected_index_set.add(index_in_data_matrix)
if self.id_is_strain:
id = id[1:-1].split(',') #id is a tuple of (ecotypeid,duplicate)
self.strain_acc_list[index_in_data_matrix] = id[0].strip()
self.category_list[index_in_data_matrix] = id[1].strip()
#else:
# self.header[index_in_data_matrix+2] = id
if self.id_is_strain:
rows_to_be_tossed_out = set(range(len(self.strain_acc_list))) - selected_index_set
write_data_matrix(self.data_matrix, output_fname, self.header,
self.strain_acc_list, self.category_list,\
rows_to_be_tossed_out, cols_to_be_tossed_out=set(), nt_alphabet=0)
else:
cols_to_be_tossed_out = set(range(len(self.header)-2)) - selected_index_set
write_data_matrix(self.data_matrix, output_fname, self.header,
self.strain_acc_list, self.category_list,
rows_to_be_tossed_out=set(),
cols_to_be_tossed_out=cols_to_be_tossed_out, nt_alphabet=0)
def show_all(self):
"""
2008-02-05
preserve the old interface. in order not to change anything in
plot_col_NA_mismatch_rate() and plot_row_NA_mismatch_rate() of QualityControl.py
"""
self.app1.show_all()
def on_button_PlotHistogram_clicked(self, widget, data=None):
"""
2016.04.14 bugfix: skip "" /empty cells
2015.01.28 add summary stats to title
2009-5-20
get the number of bins from entry_no_of_bins
2009-3-13
draw histogram of specific hist_column
2008-02-06
"""
if not getattr(self, 'columnHeaders', None):
sys.stderr.write("Nothing in columns yet.\n")
return
self.setUserDataPreprocessingFlags()
self.ax.clear()
self.canvas.mpl_disconnect(self._idClick) #drop the signal handler
self._idClick = None #reset the _idClick
hist_ls = []
hist_column = int(self.entry_hist_column.get_text())
noOfValuesDiscarded = 0
for i in range(len(self.liststore)):
x = self.liststore[i][hist_column]
if x=='': #2016.04.14 bugfix skip if empty cells #if not x:
noOfValuesDiscarded += 1
continue
x = self.processDataValue(x, self.xValuePreProcessor)
if x is None:
continue
noOfValuesDiscarded += 1
if self.xValuePreProcessor.logScale:
if x>0:
x = math.log10(x)
else:
sys.stderr.write("x value %s, not good for log10.\n"%(x))
continue
noOfValuesDiscarded += 1
hist_ls.append(x)
sys.stderr.write("WARNING: %s values were discarded.\n"%(noOfValuesDiscarded))
title = "%s %s %s"%(self.plot_title, self.columnHeaders[hist_column],
yh_matplotlib.constructTitleFromDataSummaryStat(hist_ls))
self.ax.set_title(title);
#"Histogram of %s %s"%(self.plot_title, self.columnHeaders[hist_column]))
no_of_bins = int(self.entry_no_of_bins.get_text())
#if self.x_logScale:
# self.ax.set_xscale('log')
if self.yValuePreProcessor.logScale:
self.ax.set_yscale('log')
xlabel = "(%s)"%self.columnHeaders[hist_column]
xlabel = self.decorateAxisLabel(xlabel, self.xValuePreProcessor)
if self.xValuePreProcessor.logScale:
xlabel = "log10(%s)"%(xlabel)
self.ax.set_xlabel(xlabel)
self.ax.hist(hist_ls, no_of_bins)
self.canvas.draw()
def update_no_of_selected(self, treeview, app1_appbar1):
"""
2008-02-12
to update the no_of_selected rows
(have to double click a row to change a cursor if it's multiple selection)
"""
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
return True
def parseDataHeader(self, dataHeaders=None):
"""
2016.04.15 inserted a first column to denote order of data
"""
no_of_cols = len(dataHeaders)
self.columnHeaders = ['']*(no_of_cols+1)
self.columnHeaders[0] = "0 Order"
self.columnTypes = [str]*(no_of_cols+1)
self.columnTypes[0] = int
self.columnEditableFlagList = [False]*(no_of_cols+1)
print("columnHeaders: ", self.columnHeaders)
print("columnTypes: ", self.columnTypes)
print("columnEditableFlagList: ", self.columnEditableFlagList)
for i in range(no_of_cols):
header = dataHeaders[i]
tmp_ls = header.split('|')
columnHeader = tmp_ls[0]
if len(tmp_ls)>1:
columnTypeName = tmp_ls[1]
elif i<2: #by default first two columns are of string type
columnTypeName = "string"
else: #by default columns after first two are of numeric type
columnTypeName = 'number'
column_type = self.typeName2PythonType.get(columnTypeName, str)
self.columnHeaders[i+1] = '%s %s'%(i+1, columnHeader)
self.columnTypes[i+1] = column_type
if column_type==str:
self.columnEditableFlagList[i+1] = True
print("columnHeaders: ", self.columnHeaders)
print("columnTypes: ", self.columnTypes)
print("columnEditableFlagList: ", self.columnEditableFlagList)
def readInDataToPlot(self, input_fname, sampling_probability=1.0):
"""
2016.04.15 report summary of data and inserted a first column to denote order of data
2015.04.16 use parseDataHeader()
convert each column data according to self.columnTypes
2015.01.23 added argument sampling_probability to sub-sample data
2013.07.11 use MatrixFile to read in the file
2009-5-20
add the column index into the column header for easy picking
2009-3-13
wrap the float conversion part into try...except to report what goes wrong
2009-3-13
"""
if sampling_probability>1 or sampling_probability<0:
sampling_probability=1.0
reader = MatrixFile(path=input_fname)
self.inputDataHeaders = reader.__next__()
print("delimiter: ", reader.delimiter)
print("inputDataHeaders: ", self.inputDataHeaders)
self.parseDataHeader(self.inputDataHeaders)
self.list2D = []
dimOfRawData = [0,0]
dimOfList2D = [0,0]
for row in reader:
dimOfRawData[0] += 1
dimOfRawData[1] = len(row)
if sampling_probability>0 and sampling_probability<1:
if random.random()>sampling_probability: #skip
continue
new_row = ['']*(len(row)+1) #first column is the order of data
for i in range(len(row)):
try:
new_row[i+1] = self.columnTypes[i+1](row[i])
except:
sys.stderr.write("Error in converting column %s data %s (row=%s) to type %s.\n"%\
(i, row[i], repr(row), self.columnTypes[i+1]))
sys.stderr.write('Except type: %s\n'%repr(sys.exc_info()))
traceback.print_exc()
dimOfList2D[0] += 1
dimOfList2D[1] = len(new_row)
new_row[0] = dimOfList2D[0] #order of this data
self.list2D.append(new_row)
reader.close()
sys.stderr.write("Dimension of raw data: %s. Dimension of displayed data: %s."%\
(dimOfRawData, dimOfList2D))
self.setupColumns(self.treeview_matrix)
#update status to reflect the input filename
self.app1.set_title(os.path.basename(input_fname))
self.app1_appbar1.push(input_fname)
self.plotXY(self.ax, self.canvas, self.liststore, self.plot_title)
def readInRawMatrixData(self, input_fname):
"""
2009-3-13
"""
delimiter = figureOutDelimiter(input_fname)
self.header, self.strain_acc_list, self.category_list, \
self.data_matrix = read_data(input_fname, delimiter=delimiter)
def on_imagemenuitem_open_activate(self, widget, data=None):
"""
2009-3-13
"""
self.filechooserdialog_open.show_all()
def on_button_fileopen_cancel_clicked(self, widget, data=None):
"""
2015.01.23
"""
self.filechooserdialog_open.hide()
def on_button_fileopen_ok_clicked(self, widget, data=None):
"""
2009-3-13
"""
input_fname = self.filechooserdialog_open.get_filename()
sampling_probability = float(self.entry_sampling_probability.get_text())
self.filechooserdialog_open.hide()
self.readInDataToPlot(input_fname, sampling_probability)
def on_entry_plot_title_change(self, widget, data=None):
"""
2009-3-13
upon any change in the entry_plot_title
"""
self.plot_title = self.entry_plot_title.get_text()
class DataMatrixGuiXYProbe(gtk.Window):
"""
2009-3-13
migrated from QCVisualize.py. now become a standalone program and able to read data from a file and plot ...
QCVisualize.py inherits from here
2008-02-05
embed it into a bigger gnome app, add more buttons, and change the __init__()
2008-01-01
class to visualize the results from QualityControl.py
"""
def __init__(self, plot_title='', id_is_strain=1, header=None, strain_acc_list=None, category_list=None, data_matrix=None):
"""
2008-01-10
use a paned window to wrap the scrolledwindow and the canvas
so that the relative size of canvas to the scrolledwindow could be adjusted by the user.
"""
prog = gnome.program_init('DataMatrixGuiXYProbe', '0.1') #this must be called before any initialization for gnome app
program_path = os.path.dirname(__init__.__file__) #sys.argv[0])
xml = gtk.glade.XML(os.path.join(program_path, 'DataMatrixGuiXYProbe.glade'))
xml.signal_autoconnect(self)
self.app1 = xml.get_widget("app1")
self.app1.connect("delete_event", gtk.main_quit)
self.app1.set_default_size(800, 1000)
self.app1.set_title(plot_title)
self.plot_title = plot_title
self.id_is_strain = id_is_strain
self.header = header
self.strain_acc_list = strain_acc_list
self.category_list = category_list
self.data_matrix = data_matrix
self.column_types = None
self.column_header = None
self.column_editable_flag_ls = None
self.list_2d = None
self.column_types = None
self.list_2d = None
self.column_header = None
self.editable_flag_ls = None
self.vbox1 = xml.get_widget("vbox1")
self.treeview_matrix = xml.get_widget("treeview_matrix")
# matplotlib stuff
fig = Figure(figsize=(8,8))
self.canvas = FigureCanvas(fig) # a gtk.DrawingArea
self._idClick = self.canvas.mpl_connect('button_press_event', self.on_click)
self.vpaned1 = xml.get_widget("vpaned1")
self.vpaned1.add2(self.canvas)
#vbox.pack_start(self.canvas, True, True)
self.ax = fig.add_subplot(111)
self.treeview_matrix.connect('row-activated', self.plot_row)
toolbar = NavigationToolbar(self.canvas, self.app1)
self.vbox1.pack_start(toolbar, False, False)
self.checkbutton_label_dot = xml.get_widget('checkbutton_label_dot')
self.entry_dot_label_column = xml.get_widget('entry_dot_label_column')
self.entry_x_column = xml.get_widget('entry_x_column')
self.entry_y_column = xml.get_widget('entry_y_column')
self.entry_hist_column = xml.get_widget('entry_hist_column')
self.entry_no_of_bins = xml.get_widget('entry_no_of_bins') #2009-5-20
self.entry_plot_title = xml.get_widget('entry_plot_title')
self.entry_plot_title.set_text(self.plot_title)
self.filechooserdialog_save = xml.get_widget("filechooserdialog_save")
self.filechooserdialog_save.connect("delete_event", yh_gnome.subwindow_hide)
self.filechooserdialog_open = xml.get_widget("filechooserdialog_open")
self.filechooserdialog_open.connect("delete_event", yh_gnome.subwindow_hide)
self.app1_appbar1 = xml.get_widget('app1_appbar1')
self.app1_appbar1.push('Status Message.') #import gnome.ui has to be executed.
self.treeview_matrix.connect('cursor-changed', self.update_no_of_selected, self.app1_appbar1)
self.app1.show_all()
#self.add_events(gdk.BUTTON_PRESS_MASK|gdk.KEY_PRESS_MASK|gdk.KEY_RELEASE_MASK)
def on_click(self, event):
"""
2009-3-13
use (x_lim[1]-x_lim[0])/200. as the resolution for a dot to be called identical to a data point.
similar for the y_data
2009-3-13
deal with checkbutton_label_dot, entry_dot_label_column, entry_x_column, entry_y_column
2008-01-01
derived from on_click_row() of QualityControl.py
reaction when user clicked in the plot
"""
# get the x and y coords, flip y from top to bottom
x, y = event.x, event.y
to_label_dot = self.checkbutton_label_dot.get_active()
dot_label_column = int(self.entry_dot_label_column.get_text())
x_column = int(self.entry_x_column.get_text())
y_column = int(self.entry_y_column.get_text())
x_lim = self.ax.get_xlim()
x_grain_size = (x_lim[1]-x_lim[0])/200.
y_lim = self.ax.get_ylim()
y_grain_size = (y_lim[1]-y_lim[0])/200.
if event.button==1:
if event.inaxes is not None:
print 'data coords', event.xdata, event.ydata
for row in self.list_2d:
x_data = row[x_column]
y_data = row[y_column]
if abs(x_data-event.xdata)<x_grain_size and abs(y_data-event.ydata)<y_grain_size:
info = row[dot_label_column]
if to_label_dot:
self.ax.text(event.xdata, event.ydata, info, size=8)
self.canvas.draw()
sys.stderr.write("%s: %s, %s: %s, xy=(%s, %s), info: %s.\n"%(self.column_header[0], row[0], self.column_header[1], row[1], x_data, y_data, info))
def plotXY(self, ax, canvas, liststore, plot_title='', chosen_index_ls=[]):
"""
2009-3-13
rename plot_NA_mismatch_rate to plotXY()
2008-02-05
chosen_index => chosen_index_ls
2007-12-14
"""
x_column = int(self.entry_x_column.get_text())
y_column = int(self.entry_y_column.get_text())
plot_title = self.entry_plot_title.get_text()
min_x = 1
min_y = 1
max_x = 0
max_y = 0
x_ls = []
y_ls = []
x_chosen_ls = []
y_chosen_ls = []
from sets import Set
chosen_index_set = Set(chosen_index_ls)
for i in range(len(liststore)):
row = liststore[i]
x = row[x_column]
y = row[y_column]
if x<min_x:
min_x = x
if x>max_x:
max_x = x
if y<min_y:
min_y = y
if y>max_y:
max_y = y
if i in chosen_index_set:
x_chosen_ls.append(x)
y_chosen_ls.append(y)
else:
x_ls.append(x)
y_ls.append(y)
ax.clear()
ax.plot(x_ls, y_ls, '.')
"""
#diagonal line give a rough feeling about the notion, more NA, worse calling
diagonal_start = min(min_x, min_y)-0.1
diagonal_end = max(max_x, max_x)+0.1
ax.plot([diagonal_start, diagonal_end],[diagonal_start, diagonal_end])
"""
if x_chosen_ls and y_chosen_ls: #highlight
ax.plot(x_chosen_ls, y_chosen_ls, '.', c='r')
if plot_title:
ax.set_title(plot_title)
ax.set_xlabel(self.column_header[x_column])
ax.set_ylabel(self.column_header[y_column])
canvas.draw()
def plot_row(self, treeview, path, view_column):
if self._idClick==None:
self._idClick = self.canvas.mpl_connect('button_press_event', self.on_click)
self.plotXY(self.ax, self.canvas, self.liststore, self.plot_title, path)
def setupColumns(self, treeview):
"""
2009-3-13
"""
if not getattr(self, 'column_header', None):
sys.stderr.write("Nothing in columns yet.\n")
return
self.liststore = gtk.ListStore(*self.column_types)
#self.add_columns(self.treeview_matrix)
yh_gnome.create_columns(self.treeview_matrix, self.column_header, self.editable_flag_ls, self.liststore)
yh_gnome.fill_treeview(self.treeview_matrix, self.liststore, self.list_2d, reorderable=True)
self.treeselection = self.treeview_matrix.get_selection()
def on_button_highlight_clicked(self, widget, data=None):
"""
2008-02-12
to update the no_of_selected rows (have to double click a row to change a cursor if it's multiple selection)
2008-02-05
"""
if self._idClick==None:
self._idClick = self.canvas.mpl_connect('button_press_event', self.on_click)
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
index_ls = []
for path in pathlist_strains1:
index_ls.append(path[0])
self.app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
self.plotXY(self.ax, self.canvas, self.liststore, self.plot_title, index_ls)
def on_button_save_clicked(self, widget, data=None):
"""
2008-02-05
"""
self.filechooserdialog_save.show_all()
def on_button_filechooserdialog_cancel_ok_clicked(self, widget, data=None):
"""
2008-02-05
"""
self.filechooserdialog_save.hide()
def on_button_filechooserdialog_save_ok_clicked(self, widget, data=None):
"""
2008-02-12
to update the no_of_selected rows (have to double click a row to change a cursor if it's multiple selection)
2008-02-05
"""
output_fname = self.filechooserdialog_save.get_filename()
self.filechooserdialog_save.hide()
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
self.app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
if self.header and self.strain_acc_list and self.category_list and self.data_matrix:
selected_index_set = Set()
for path in pathlist_strains1:
row = self.liststore[path[0]]
id = row[0]
index_in_data_matrix = row[-1]
selected_index_set.add(index_in_data_matrix)
if self.id_is_strain:
id = id[1:-1].split(',') #id is a tuple of (ecotypeid,duplicate)
self.strain_acc_list[index_in_data_matrix] = id[0].strip() #remove extra space
self.category_list[index_in_data_matrix] = id[1].strip()
#else:
# self.header[index_in_data_matrix+2] = id
from variation.src.FilterStrainSNPMatrix import FilterStrainSNPMatrix
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
if self.id_is_strain:
rows_to_be_tossed_out = Set(range(len(self.strain_acc_list))) - selected_index_set
FilterStrainSNPMatrix_instance.write_data_matrix(self.data_matrix, output_fname, self.header, self.strain_acc_list, self.category_list,\
rows_to_be_tossed_out, cols_to_be_tossed_out=Set(), nt_alphabet=0)
else:
cols_to_be_tossed_out = Set(range(len(self.header)-2)) - selected_index_set
FilterStrainSNPMatrix_instance.write_data_matrix(self.data_matrix, output_fname, self.header, self.strain_acc_list, self.category_list,\
rows_to_be_tossed_out=Set(), cols_to_be_tossed_out=cols_to_be_tossed_out, nt_alphabet=0)
def show_all(self):
"""
2008-02-05
preserve the old interface. in order not to change anything in plot_col_NA_mismatch_rate() and plot_row_NA_mismatch_rate() of QualityControl.py
"""
self.app1.show_all()
def on_button_histogram_clicked(self, widget, data=None):
"""
2009-5-20
get the number of bins from entry_no_of_bins
2009-3-13
draw histogram of specific hist_column
2008-02-06
"""
if not getattr(self, 'column_header', None):
sys.stderr.write("Nothing in columns yet.\n")
return
self.ax.clear()
self.canvas.mpl_disconnect(self._idClick) #drop the signal handler
self._idClick = None #reset the _idClick
hist_ls = []
hist_column = int(self.entry_hist_column.get_text())
for i in range(len(self.liststore)):
hist_ls.append(self.liststore[i][hist_column])
self.ax.set_title("Histogram of %s %s"%(self.plot_title, self.column_header[hist_column]))
no_of_bins = int(self.entry_no_of_bins.get_text())
self.ax.hist(hist_ls, no_of_bins)
self.canvas.draw()
def update_no_of_selected(self, treeview, app1_appbar1):
"""
2008-02-12
to update the no_of_selected rows (have to double click a row to change a cursor if it's multiple selection)
"""
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
return True
def readInDataToPlot(self, input_fname):
"""
2009-5-20
add the column index into the column header for easy picking
2009-3-13
wrap the float conversion part into try...except to report what goes wrong
2009-3-13
"""
reader = csv.reader(open(input_fname), delimiter=figureOutDelimiter(input_fname))
self.column_header=reader.next()
for i in range(len(self.column_header)):
self.column_header[i] = '%s %s'%(i, self.column_header[i])
no_of_cols = len(self.column_header)
self.column_types = [str]*2 + [float]*(no_of_cols-2)
self.column_editable_flag_ls = [True, True] + [False]*(no_of_cols-2)
self.list_2d = []
for row in reader:
float_part = row[2:]
try:
float_part = map(float, float_part)
except:
sys.stderr.write('Except type: %s\n'%repr(sys.exc_info()))
traceback.print_exc()
new_row = row[:2]+float_part
self.list_2d.append(new_row)
self.setupColumns(self.treeview_matrix)
self.plotXY(self.ax, self.canvas, self.liststore, self.plot_title)
def readInRawMatrixData(self, input_fname):
"""
2009-3-13
"""
delimiter = figureOutDelimiter(input_fname)
self.header, self.strain_acc_list, self.category_list, self.data_matrix = read_data(input_fname, delimiter=delimiter)
def on_imagemenuitem_open_activate(self, widget, data=None):
"""
2009-3-13
"""
self.filechooserdialog_open.show_all()
def on_button_fileopen_ok_clicked(self, widget, data=None):
"""
2009-3-13
"""
input_fname = self.filechooserdialog_open.get_filename()
self.filechooserdialog_open.hide()
self.readInDataToPlot(input_fname)
def on_entry_plot_title_change(self, widget, data=None):
"""
2009-3-13
upon any change in the entry_plot_title
"""
self.plot_title = self.entry_plot_title.get_text()
class DataMatrixGuiXYProbe(gtk.Window):
"""
2009-3-13
migrated from QCVisualize.py. now become a standalone program and able to read data from a file and plot ...
QCVisualize.py inherits from here
2008-02-05
embed it into a bigger gnome app, add more buttons, and change the __init__()
2008-01-01
class to visualize the results from QualityControl.py
"""
def __init__(self, plot_title='', id_is_strain=1, header=None, strain_acc_list=None, category_list=None, data_matrix=None):
"""
2008-01-10
use a paned window to wrap the scrolledwindow and the canvas
so that the relative size of canvas to the scrolledwindow could be adjusted by the user.
"""
prog = gnome.program_init('DataMatrixGuiXYProbe', '0.1') #this must be called before any initialization for gnome app
program_path = os.path.dirname(__init__.__file__) #sys.argv[0])
xml = gtk.glade.XML(os.path.join(program_path, 'DataMatrixGuiXYProbe.glade'))
xml.signal_autoconnect(self)
self.app1 = xml.get_widget("app1")
self.app1.connect("delete_event", gtk.main_quit)
self.app1.set_default_size(800, 1000)
self.app1.set_title(plot_title)
self.plot_title = plot_title
self.id_is_strain = id_is_strain
self.header = header
self.strain_acc_list = strain_acc_list
self.category_list = category_list
self.data_matrix = data_matrix
self.column_types = None
self.column_header = None
self.column_editable_flag_ls = None
self.list_2d = None
self.column_types = None
self.list_2d = None
self.column_header = None
self.editable_flag_ls = None
self.vbox1 = xml.get_widget("vbox1")
self.treeview_matrix = xml.get_widget("treeview_matrix")
# matplotlib stuff
fig = Figure(figsize=(8,8))
self.canvas = FigureCanvas(fig) # a gtk.DrawingArea
self._idClick = self.canvas.mpl_connect('button_press_event', self.onUserClickCanvas)
self.vpaned1 = xml.get_widget("vpaned1")
self.vpaned1.add2(self.canvas)
#vbox.pack_start(self.canvas, True, True)
self.ax = fig.add_subplot(111)
self.treeview_matrix.connect('row-activated', self.plot_row)
toolbar = NavigationToolbar(self.canvas, self.app1)
self.vbox1.pack_start(toolbar, False, False)
self.checkbutton_label_dot = xml.get_widget('checkbutton_label_dot')
self.entry_dot_label_column = xml.get_widget('entry_dot_label_column')
self.entry_x_na = xml.get_widget('entry_x_na')
self.entry_y_na = xml.get_widget('entry_y_na')
self.entry_multiply_x = xml.get_widget('entry_multiply_x')
self.entry_multiply_y = xml.get_widget('entry_multiply_y')
self.entry_add_x = xml.get_widget('entry_add_x')
self.entry_add_y = xml.get_widget('entry_add_y')
self.entry_x_error = xml.get_widget("entry_x_error")
self.entry_y_error = xml.get_widget("entry_y_error")
self.checkbutton_logX = xml.get_widget('checkbutton_logX') #2014.06.09
self.checkbutton_logY = xml.get_widget('checkbutton_logY')
self.entry_x_column = xml.get_widget('entry_x_column')
self.entry_y_column = xml.get_widget('entry_y_column')
#self.checkbutton_histLogX = xml.get_widget('checkbutton_histLogX') #2014.06.09
#self.checkbutton_histLogY = xml.get_widget('checkbutton_histLogY')
self.entry_hist_column = xml.get_widget('entry_hist_column')
self.entry_no_of_bins = xml.get_widget('entry_no_of_bins') #2009-5-20
self.entry_plot_title = xml.get_widget('entry_plot_title')
self.entry_plot_title.set_text(self.plot_title)
self.filechooserdialog_save = xml.get_widget("filechooserdialog_save")
self.filechooserdialog_save.connect("delete_event", yh_gnome.subwindow_hide)
self.entry_sampling_probability = xml.get_widget("entry_sampling_probability")
self.filechooserdialog_open = xml.get_widget("filechooserdialog_open")
self.filechooserdialog_open.connect("delete_event", yh_gnome.subwindow_hide)
self.app1_appbar1 = xml.get_widget('app1_appbar1')
self.app1_appbar1.push('Status Message.') #import gnome.ui has to be executed.
self.treeview_matrix.connect('cursor-changed', self.update_no_of_selected, self.app1_appbar1)
self.app1.show_all()
self.xValuePreProcessor = None
self.yValuePreProcessor = None
self.x_error_column_index = None
self.y_error_column_index = None
#self.add_events(gdk.BUTTON_PRESS_MASK|gdk.KEY_PRESS_MASK|gdk.KEY_RELEASE_MASK)
def onUserClickCanvas(self, event):
"""
2009-3-13
use (x_lim[1]-x_lim[0])/200. as the resolution for a dot to be called identical to a data point.
similar for the y_data
2009-3-13
deal with checkbutton_label_dot, entry_dot_label_column, entry_x_column, entry_y_column
2008-01-01
derived from on_click_row() of QualityControl.py
reaction when user clicked in the plot
"""
# get the x and y coords, flip y from top to bottom
x, y = event.x, event.y
to_label_dot = self.checkbutton_label_dot.get_active()
dot_label_column = int(self.entry_dot_label_column.get_text())
x_column = int(self.entry_x_column.get_text())
y_column = int(self.entry_y_column.get_text())
x_lim = self.ax.get_xlim()
x_grain_size = (x_lim[1]-x_lim[0])/200.
y_lim = self.ax.get_ylim()
y_grain_size = (y_lim[1]-y_lim[0])/200.
if event.button==1:
if event.inaxes is not None:
print 'data coords', event.xdata, event.ydata
if self.list_2d is None:
return
for row in self.list_2d:
if row[x_column] and row[y_column]: #not empty
try:
x_data = float(row[x_column])
y_data = float(row[y_column])
x = self.processDataValue(x_data, self.xValuePreProcessor)
if x is None:
continue
y = self.processDataValue(y_data, self.yValuePreProcessor)
if y is None:
continue
if abs(x-event.xdata)<x_grain_size and abs(y-event.ydata)<y_grain_size:
info = row[dot_label_column]
if to_label_dot:
self.ax.text(event.xdata, event.ydata, info, size=8)
self.canvas.draw()
sys.stderr.write("%s: %s, %s: %s, raw xy=(%s, %s), scaled xy=(%s,%s), info: %s.\n"%\
(self.column_header[0], row[0], self.column_header[1], row[1], row[x_column], row[y_column], x,y, info))
except:
sys.stderr.write("Column %s, %s of row (%s), could not be converted to float. skip.\n"%\
(x_column, y_column, repr(row)))
def setUserDataPreprocessingFlags(self):
"""
2014.07.25
"""
self.xValuePreProcessor = ValuePreProcessor(na = self.entry_x_na.get_text())
self.yValuePreProcessor = ValuePreProcessor(na = self.entry_y_na.get_text())
if self.entry_multiply_x.get_text():
self.xValuePreProcessor.scalar = float(self.entry_multiply_x.get_text())
if self.entry_multiply_y.get_text():
self.yValuePreProcessor.scalar = float(self.entry_multiply_y.get_text())
if self.entry_add_x.get_text():
self.xValuePreProcessor.addition = float(self.entry_add_x.get_text())
if self.entry_add_y.get_text():
self.yValuePreProcessor.addition = float(self.entry_add_y.get_text())
if self.entry_x_error.get_text():
self.xValuePreProcessor.errorColumnIndex = int(self.entry_x_error.get_text())
if self.entry_y_error.get_text():
self.yValuePreProcessor.errorColumnIndex = int(self.entry_y_error.get_text())
if self.checkbutton_logX.get_active():
self.xValuePreProcessor.logScale = True
if self.checkbutton_logY.get_active():
self.yValuePreProcessor.logScale = True
def processDataValue(self, value=None, valuePreProcessor=None):
"""
2014.07.31
"""
if valuePreProcessor.na is not None and (value==valuePreProcessor.na or float(value)==float(valuePreProcessor.na)):
return None
value = float(value)
if valuePreProcessor.scalar is not None:
value = value*valuePreProcessor.scalar
if valuePreProcessor.addition is not None:
value = value + valuePreProcessor.addition
return value
def decorateAxisLabel(self, label=None, valuePreProcessor=None):
"""
2014.07.31
"""
if valuePreProcessor.scalar is not None:
label = "%s*%s"%(valuePreProcessor.scalar, label)
if valuePreProcessor.addition:
label = "%s+%s"%(label, valuePreProcessor.addition)
return label
def plotXY(self, ax, canvas, liststore, plot_title='',
chosen_index_ls=[]):
"""
2015.01.28 add summary stats to title
2014.04.29 add error bars
2009-3-13
rename plot_NA_mismatch_rate to plotXY()
2008-02-05
chosen_index => chosen_index_ls
2007-12-14
"""
x_column = int(self.entry_x_column.get_text())
y_column = int(self.entry_y_column.get_text())
self.setUserDataPreprocessingFlags()
plot_title = self.entry_plot_title.get_text()
min_x = 1
min_y = 1
max_x = 0
max_y = 0
x_ls = []
x_error_ls = []
y_ls = []
y_error_ls = []
x_chosen_ls = []
x_chosen_error_ls = []
y_chosen_ls = []
y_chosen_error_ls = []
chosen_index_set = set(chosen_index_ls)
for i in range(len(liststore)):
row = liststore[i]
x = row[x_column]
y = row[y_column]
if not x or not y: #2013.07.12 skip if empty cells
continue
x = self.processDataValue(x, self.xValuePreProcessor)
if x is None:
continue
y = self.processDataValue(y, self.yValuePreProcessor)
if y is None:
continue
if self.xValuePreProcessor.errorColumnIndex is not None:
x_error = row[self.xValuePreProcessor.errorColumnIndex]
else:
x_error = 0
if self.yValuePreProcessor.errorColumnIndex is not None:
y_error = row[self.yValuePreProcessor.errorColumnIndex]
else:
y_error = 0
if x<min_x:
min_x = x
if x>max_x:
max_x = x
if y<min_y:
min_y = y
if y>max_y:
max_y = y
if i in chosen_index_set:
x_chosen_ls.append(x)
y_chosen_ls.append(y)
x_chosen_error_ls.append(x_error)
y_chosen_error_ls.append(y_error)
else:
x_ls.append(x)
y_ls.append(y)
x_error_ls.append(x_error)
y_error_ls.append(y_error)
ax.clear()
if self.xValuePreProcessor.logScale:
ax.set_xscale('log')
if self.yValuePreProcessor.logScale:
ax.set_yscale('log')
if self.x_error_column_index is not None and self.y_error_column_index is not None:
ax.errorbar(x_ls, y_ls, xerr=x_error_ls, yerr=y_error_ls, ecolor='g', fmt='o')
else:
ax.plot(x_ls, y_ls, '.')
"""
#diagonal line give a rough feeling about the notion, more NA, worse calling
diagonal_start = min(min_x, min_y)-0.1
diagonal_end = max(max_x, max_x)+0.1
ax.plot([diagonal_start, diagonal_end],[diagonal_start, diagonal_end])
"""
if x_chosen_ls and y_chosen_ls: #highlight
titleWithStats = "Highlighted data\n" + yh_matplotlib.constructTitleFromTwoDataSummaryStat(x_chosen_ls, y_chosen_ls)
ax.plot(x_chosen_ls, y_chosen_ls, '.', c='r')
if self.x_error_column_index is not None and self.y_error_column_index is not None:
ax.errorbar(x_chosen_ls, y_chosen_ls, xerr=x_chosen_error_ls, yerr=y_chosen_error_ls, ecolor='r', color='r', fmt='o')
else: #take all data
titleWithStats = yh_matplotlib.constructTitleFromTwoDataSummaryStat(x_ls+x_chosen_ls, y_ls+y_chosen_ls)
if plot_title:
ax.set_title("%s %s"%(plot_title, titleWithStats))
else:
ax.set_title(titleWithStats)
xlabel = "(%s)"%self.column_header[x_column]
xlabel = self.decorateAxisLabel(xlabel, self.xValuePreProcessor)
ax.set_xlabel(xlabel)
ylabel = "(%s)"%self.column_header[y_column]
ylabel = self.decorateAxisLabel(ylabel, self.yValuePreProcessor)
ax.set_ylabel(ylabel)
canvas.draw()
def plot_row(self, treeview, path, view_column):
if self._idClick==None:
self._idClick = self.canvas.mpl_connect('button_press_event', self.onUserClickCanvas)
self.plotXY(self.ax, self.canvas, self.liststore, self.plot_title, path)
def setupColumns(self, treeview):
"""
2009-3-13
"""
if not getattr(self, 'column_header', None):
sys.stderr.write("Nothing in columns yet.\n")
return
self.liststore = gtk.ListStore(*self.column_types)
#self.add_columns(self.treeview_matrix)
yh_gnome.create_columns(self.treeview_matrix, self.column_header, self.editable_flag_ls, self.liststore)
yh_gnome.fill_treeview(self.treeview_matrix, self.liststore, self.list_2d, reorderable=True)
self.treeselection = self.treeview_matrix.get_selection()
def on_button_PlotXY_clicked(self, widget, data=None):
"""
2008-02-12
to update the no_of_selected rows (have to double click a row to change a cursor if it's multiple selection)
2008-02-05
"""
if self._idClick==None:
self._idClick = self.canvas.mpl_connect('button_press_event', self.onUserClickCanvas)
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
index_ls = []
for path in pathlist_strains1:
index_ls.append(path[0])
self.app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
self.plotXY(self.ax, self.canvas, self.liststore, self.plot_title, index_ls)
def on_button_save_clicked(self, widget, data=None):
"""
2008-02-05
"""
self.filechooserdialog_save.show_all()
def on_button_filechooserdialog_cancel_ok_clicked(self, widget, data=None):
"""
2008-02-05
"""
self.filechooserdialog_save.hide()
def on_button_filechooserdialog_save_ok_clicked(self, widget, data=None):
"""
2008-02-12
to update the no_of_selected rows (have to double click a row to change a cursor if it's multiple selection)
2008-02-05
"""
output_fname = self.filechooserdialog_save.get_filename()
self.filechooserdialog_save.hide()
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
self.app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
if self.header and self.strain_acc_list and self.category_list and self.data_matrix:
selected_index_set = set()
for path in pathlist_strains1:
row = self.liststore[path[0]]
id = row[0]
index_in_data_matrix = row[-1]
selected_index_set.add(index_in_data_matrix)
if self.id_is_strain:
id = id[1:-1].split(',') #id is a tuple of (ecotypeid,duplicate)
self.strain_acc_list[index_in_data_matrix] = id[0].strip() #remove extra space
self.category_list[index_in_data_matrix] = id[1].strip()
#else:
# self.header[index_in_data_matrix+2] = id
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
if self.id_is_strain:
rows_to_be_tossed_out = set(range(len(self.strain_acc_list))) - selected_index_set
FilterStrainSNPMatrix_instance.write_data_matrix(self.data_matrix, output_fname, self.header, self.strain_acc_list, self.category_list,\
rows_to_be_tossed_out, cols_to_be_tossed_out=set(), nt_alphabet=0)
else:
cols_to_be_tossed_out = set(range(len(self.header)-2)) - selected_index_set
FilterStrainSNPMatrix_instance.write_data_matrix(self.data_matrix, output_fname, self.header, self.strain_acc_list, self.category_list,\
rows_to_be_tossed_out=set(), cols_to_be_tossed_out=cols_to_be_tossed_out, nt_alphabet=0)
def show_all(self):
"""
2008-02-05
preserve the old interface. in order not to change anything in plot_col_NA_mismatch_rate() and plot_row_NA_mismatch_rate() of QualityControl.py
"""
self.app1.show_all()
def on_button_PlotHistogram_clicked(self, widget, data=None):
"""
2015.01.28 add summary stats to title
2009-5-20
get the number of bins from entry_no_of_bins
2009-3-13
draw histogram of specific hist_column
2008-02-06
"""
if not getattr(self, 'column_header', None):
sys.stderr.write("Nothing in columns yet.\n")
return
self.setUserDataPreprocessingFlags()
self.ax.clear()
self.canvas.mpl_disconnect(self._idClick) #drop the signal handler
self._idClick = None #reset the _idClick
hist_ls = []
hist_column = int(self.entry_hist_column.get_text())
for i in range(len(self.liststore)):
x = self.liststore[i][hist_column]
if not x:
continue
x = self.processDataValue(x, self.xValuePreProcessor)
if x is None:
continue
if self.xValuePreProcessor.logScale:
if x>0:
x = math.log10(x)
else:
sys.stderr.write("x value %s, not good for log10.\n"%(x))
continue
hist_ls.append(x)
title = "%s %s %s"%(self.plot_title, self.column_header[hist_column],
yh_matplotlib.constructTitleFromDataSummaryStat(hist_ls))
self.ax.set_title(title); #"Histogram of %s %s"%(self.plot_title, self.column_header[hist_column]))
no_of_bins = int(self.entry_no_of_bins.get_text())
#if self.x_logScale:
# self.ax.set_xscale('log')
if self.yValuePreProcessor.logScale:
self.ax.set_yscale('log')
xlabel = "(%s)"%self.column_header[hist_column]
xlabel = self.decorateAxisLabel(xlabel, self.xValuePreProcessor)
if self.xValuePreProcessor.logScale:
xlabel = "log10(%s)"%(xlabel)
self.ax.set_xlabel(xlabel)
self.ax.hist(hist_ls, no_of_bins)
self.canvas.draw()
def update_no_of_selected(self, treeview, app1_appbar1):
"""
2008-02-12
to update the no_of_selected rows (have to double click a row to change a cursor if it's multiple selection)
"""
pathlist_strains1 = []
self.treeselection.selected_foreach(yh_gnome.foreach_cb, pathlist_strains1)
app1_appbar1.push("%s rows selected."%len(pathlist_strains1))
return True
def readInDataToPlot(self, input_fname, sampling_probability=1.0):
"""
2015.01.23 added argument sampling_probability to sub-sample data
2013.07.11 use MatrixFile to read in the file
2009-5-20
add the column index into the column header for easy picking
2009-3-13
wrap the float conversion part into try...except to report what goes wrong
2009-3-13
"""
if sampling_probability>1 or sampling_probability<0:
sampling_probability=1.0
reader = MatrixFile(inputFname=input_fname)
self.column_header=reader.next()
for i in range(len(self.column_header)):
self.column_header[i] = '%s %s'%(i, self.column_header[i])
no_of_cols = len(self.column_header)
self.column_types = [str]*2 + [float]*(no_of_cols-2)
self.column_editable_flag_ls = [True, True] + [False]*(no_of_cols-2)
self.list_2d = []
for row in reader:
if sampling_probability>0 and sampling_probability<1:
if random.random()>sampling_probability: #skip
continue
float_part = row[2:]
try:
float_part = map(float, float_part)
except:
sys.stderr.write('Except type: %s\n'%repr(sys.exc_info()))
traceback.print_exc()
new_row = row[:2]+float_part
self.list_2d.append(new_row)
reader.close()
self.setupColumns(self.treeview_matrix)
#update status to reflect the input filename
self.app1.set_title(os.path.basename(input_fname))
self.app1_appbar1.push(input_fname)
self.plotXY(self.ax, self.canvas, self.liststore, self.plot_title)
def readInRawMatrixData(self, input_fname):
"""
2009-3-13
"""
delimiter = figureOutDelimiter(input_fname)
self.header, self.strain_acc_list, self.category_list, self.data_matrix = read_data(input_fname, delimiter=delimiter)
def on_imagemenuitem_open_activate(self, widget, data=None):
"""
2009-3-13
"""
self.filechooserdialog_open.show_all()
def on_button_fileopen_cancel_clicked(self, widget, data=None):
"""
2015.01.23
"""
self.filechooserdialog_open.hide()
def on_button_fileopen_ok_clicked(self, widget, data=None):
"""
2009-3-13
"""
input_fname = self.filechooserdialog_open.get_filename()
sampling_probability = float(self.entry_sampling_probability.get_text())
self.filechooserdialog_open.hide()
self.readInDataToPlot(input_fname, sampling_probability)
def on_entry_plot_title_change(self, widget, data=None):
"""
2009-3-13
upon any change in the entry_plot_title
"""
self.plot_title = self.entry_plot_title.get_text()
class MainView(BasePlotView, gtk.Frame):
"""
A Gtk Frame based plotting widget for dreampy
that contains additional tool bar items for printing
and adding notes
"""
def __init__(self, win, **kwargs):
gtk.Frame.__init__(self)
BasePlotView.__init__(self, **kwargs)
self.win = win
self.title = None
#Put some stuff
# self.suppress_header = kwargs.get('suppress_header', False)
# self.suppress_title = kwargs.get('suppress_title', False)
# self.suppress_legend = kwargs.get('suppress_legend', False)
self.vbox = gtk.VBox(False, 0)
self.add(self.vbox)
self.sw = gtk.ScrolledWindow()
self.sw.set_policy(gtk.POLICY_AUTOMATIC, gtk.POLICY_AUTOMATIC)
self.vbox.pack_start(self.sw, True, True, 0)
self.sw.show()
self.f = Figure(figsize=(5,4), dpi=100)
self.canvas = FigureCanvas(self.f) # a gtk.DrawingArea
self.canvas.set_size_request(400,300)
self.sw.add_with_viewport (self.canvas)
self.canvas.show_all()
self.toolbar = NavToolBar(self.canvas, self.win)
self.vbox.pack_start(self.toolbar, False, False)
self.toolbar.show()
self.vbox.show()
# self.autoscale = True
# self.xmin = None
# self.xmax = None
# self.ymin = None
# self.ymax = None
# self.image = None
# self.hold_plot = False
# self.keyid = None
# self.filter = None
# self.labelsize = 8
# self.titlesize = 10
# self.ticklabelsize = 8
# self.ticklabelweight = 'normal'
# self.labelweight = 'bold'
# self.titleweight = 'bold'
# self.legendsize = 8
# self.legendweight = 'normal'
# self.hdrlabelsize = 9
# self.hdrlabelweight = 'normal'
# self.cur_axname = None
self.refresh_canvas()
self.show_all()
#self.gtk_catchup()
def gtk_catchup(self):
gtk.gdk.threads_enter()
while gtk.events_pending():
gtk.main_iteration()
gtk.gdk.threads_leave()
def create_arrow_button(self, arrow_type, shadow_type):
button = gtk.Button()
self.arrow = gtk.Arrow(arrow_type, shadow_type)
button.add(self.arrow)
button.show()
self.arrow.show()
return button
def list_widgets_turnoff(self):
self.left_button.set_sensitive(False)
self.right_button.set_sensitive(False)
self.ignore_button.set_sensitive(False)
#if self.keyid:
# self.canvas.disconnect(self.keyid)
def disconnect_event(self, sig):
if self.canvas:
self.canvas.mpl_disconnect(sig)
def connect_event(self, eventname, eventfunc):
if self.canvas:
self.canvas.set_flags(gtk.CAN_FOCUS) #to grab focus for keystrokes
self.canvas.grab_focus() #to grab focus for keystrokes
return self.canvas.mpl_connect(eventname, eventfunc)
def redraw_plot(self):
if self.hold_plot is False:
if hasattr(self.canvas, 'show_all'):
self.canvas.show_all()
self.canvas.draw()
self.gtk_catchup()
