def RedrawBarChart(master,
loadSequences,
_position=None,
_seq=None,
_set_ids=None,
_elements=None,
_heatMapSize=None,
_ranges=None):
cur_window_size = -1
bin_start = None
bin_stop = None
if (len(master.SetIdList) > 0):
cur_shift_size = master.SetIdList[0].split("_")[2]
#master.button5["state"] = DISABLED
if (_position == None):
try:
master.root.canvas.delete('all')
except Exception:
pass
if (master.image_export_possible == True):
master.draw.rectangle(
(0, 0, master.image1Width, master.image1Height), fill="white")
master.lineChart = False
master.focusOnBarCharts = 1
if (_heatMapSize == None):
master.heatMapSize = 100
else:
master.heatMapSize = _heatMapSize
master.pswidth = 0
master.pswidthExport = 0
master.psheight = 0
barChart = {}
real_max = -1
if (_seq != None):
master.seq_ids = []
master.seq_ids.append(_seq)
if (_set_ids != None):
master.SetIdList = _set_ids
max_value = -1
max_value_total = -1
l = 0
if (len(master.SetIdList) > 0):
for seq in master.seq_ids:
if (_ranges != None and l < len(_ranges)):
bin_start = int(int(_ranges[l]) * 1000000)
master.bin_start = (bin_start / 1000000)
bin_stop = int(int(_ranges[l + 1]) * 1000000)
l = l + 2
counter = 0
elements_total = None
for value in master.SetIdList:
if (master.cmd_line == False):
master.display = "% bp"
elements = None
#master.NContent.set(100)
if (_elements == None):
elements = master.getElementsFromDatabase(
seq, value, master.density_table, master.db_file,
bin_start, bin_stop)[0]
if (master.display != "% bp"):
if (elements_total == None):
elements_total = [0] * (len(elements))
for i in range(0, len(elements)):
elements_total[i] = elements_total[i] + elements[i]
elements[i] = (elements[i])
else:
elements = _elements[value]
if (barChart.get(seq) == None):
barChart[seq] = {}
barChart[seq][counter] = []
barChart[seq][counter] = elements
if (master.colorToSetIdMap.get(value) != None):
master.colorMap[counter] = master.colorToSetIdMap.get(
value)
else:
master.colorMap[counter] = master.colors[counter % len(
master.colors)]
master.colorToSetIdMap[value] = master.colors[
counter % len(master.colors)]
counter = counter + 1
if (master.cmd_line == True and master.display != "% bp"):
max_value = max(elements_total)
if (max_value_total < max_value):
max_value_total = max_value
real_max = max_value_total
if (master.cmd_line == True and master.display != "% bp"):
for seq in master.seq_ids:
amountElements = len((barChart.get(seq)).get(0))
for i in range(0, amountElements):
sum = 0
for k in range(0, len(barChart.get(seq).keys())):
barChart[seq].get(k)[i] = int(
(barChart[seq].get(k)[i] / float(real_max)) *
100.0)
position = 0
if (_position != None):
position = _position
x = 0
for seq in master.seq_ids:
if (_ranges != None and x < len(_ranges)):
bin_start = int(int(_ranges[x]) * 1000000)
master.bin_start = (bin_start / 1000000)
x = x + 2
amountElements = len((barChart.get(seq)).get(0))
for i in range(0, amountElements):
sum = 0
for k in range(1, len(barChart.get(seq).keys())):
barChart[seq].get(k)[i] += barChart[seq].get(k - 1)[i]
barChart[seq][counter] = []
master.colorMap[counter] = master.colorBackGround
for l in range(0, amountElements):
barChart.get(seq).get(counter).append(100)
keys = []
keys = barChart[seq].keys()
keys.reverse()
master.AdaptMaxLabelSize()
for ckey in keys:
if (len(seq) * master.fontSize > master.maxLabelSize):
master.maxLabelSize = len(seq) * master.fontSize
elements = barChart.get(seq).get(ckey)
for i in range(0, len(elements)):
elements[i] = elements[i] * master.heatMapSize / 100.0
calc_vis_elements.calc_vis_elements(master, elements, seq,
position, 1, True, False,
master.colorMap.get(ckey),
"", None, None, real_max)
position = position + 1
if (_position != None):
return
calc_vis_elements.createBarChartLegend(master, "BarChart")
master.ChangeSize()
if (master.scale != None):
master.scale.destroy()
master.scale = None
if (master.button != None):
master.button.destroy()
master.button = None
def RedrawHeatmap(master, _ranges=None):
try:
master.root.canvas.delete('all')
except Exception:
pass
if (master.image_export_possible == True):
master.draw.rectangle((0, 0, master.image1Width, master.image1Height),
fill="white")
bin_start = None
bin_stop = None
master.heatMapSize = 75
master.focusOnBarCharts = 0
position = 1
mode = master.display
master.pswidth = 0
master.pswidthExport = 0
master.AdaptMaxLabelSize()
try:
master.getMax2()
except Exception:
pass
absolute_max = master.maxV
absolute_min = master.minV
try:
master.scale["to"] = math.ceil(absolute_max)
master.scale["from"] = math.ceil(absolute_min)
except Exception:
pass
l = 0
for seq_id in master.seq_ids:
elements = []
if (_ranges != None and l < len(_ranges)):
bin_start = int(int(_ranges[l]) * 1000000)
master.bin_start = (bin_start / 1000000)
bin_stop = int(int(_ranges[l + 1]) * 1000000)
l = l + 2
if (master.elementList.get(seq_id) == None or _ranges != None):
elements = master.getElementsFromDatabase(seq_id, master.set_id_A,
master.density_table,
master.db_file,
bin_start, bin_stop)[0]
master.elementList[seq_id] = elements
else:
elements = master.elementList.get(seq_id)
try:
scaleValue = master.scale.get()
if (scaleValue == 0):
scaleValue = master.maxV
except Exception:
scaleValue = master.maxV
#SCALING PARAMETER
scaleValue = 100 #damit heatmap colors zw. 0 und 100 prozent skaliert
if (scaleValue - absolute_min == 0):
intensityF = absolute_max / absolute_min
elif (scaleValue - absolute_min < 0):
intensityF = 0
else:
intensityF = (absolute_max - absolute_min) / (scaleValue -
absolute_min)
calc_vis_elements.calc_vis_elements(master, elements, seq_id, position,
intensityF, False, False, False,
"", absolute_min, absolute_max,
None)
position = position + 1
if len(master.seq_ids) > 0:
calc_vis_elements.createColorMap(master, mode)
def RedrawStackedHeatmap(master, heatMapSize=None, _ranges=None):
try:
master.button5["state"] = NORMAL
master.root.canvas.delete('all')
if (master.image_export_possible == True):
master.draw.rectangle(
(0, 0, master.image1Width, master.image1Height), fill="white")
except Exception:
pass
master.lineChart = False
master.pswidth = 0
master.psheight = 0
master.gapBetweenHeatmaps = 0
if (heatMapSize == None):
master.heatMapSize = 50
else:
master.heatMapSize = heatMapSize
position = 0
master.focusOnBarCharts = 2
seq_ids = master.seq_ids
anno_ids = master.anno_ids
master.AdaptMaxLabelSize()
l = 0
bin_start = None
bin_stop = None
for seq_id in seq_ids:
if (_ranges != None and l < len(_ranges)):
bin_start = int(int(_ranges[l]) * 1000000)
bin_stop = int(int(_ranges[l + 1]) * 1000000)
l = l + 2
for anno_id in anno_ids:
master.set_id_A = anno_id
try:
minIntensity = None
maxIntensity = None
try:
master.calculateMinAndMax()
print "anno_id::", anno_id, seq_id
minIntensity = master.anno_ids_mItensities[anno_id]["min"]
maxIntensity = master.anno_ids_mItensities[anno_id]["max"]
print "max:", maxIntensity, "min:", minIntensity
print "\n\n"
except Exception:
print "ERROR", "RedrawStackedHeatmap", sys.exc_info()
cIntensity = None
filterOn = False
try:
cIntensity = master.anno_ids_mItensities[seq_id]["cur"]
print "INFO", "using seq_id constraint", cIntensity, "for seq_id", seq_id
filterOn = True
except Exception:
pass
try:
cIntensity = master.anno_ids_mItensities[anno_id]["cur"]
print "INFO", "using set_id constraint", cIntensity, "for set_id", anno_id
filterOn = True
except Exception:
pass
try:
cIntensity = master.anno_ids_mItensities[seq_id + "_" +
anno_id]["cur"]
filterOn = True
print "INFO", "using seq_id+set_id constraint", cIntensity, "for set_id", anno_id
except Exception:
pass
#
elements = master.getElementsFromDatabase(
seq_id, anno_id, master.density_table, master.db_file,
bin_start, bin_stop)[0]
#
if (cIntensity == None):
print "INFO", "cIntensity>maxIntensity", maxIntensity
cIntensity = maxIntensity
elif (int(cIntensity) == -1):
print "INFO", "using track max", max(elements)
cIntensity = max(elements)
#
if (filterOn == True):
intensity = max(elements) / cIntensity
else:
intensity = max(elements) / maxIntensity
#
if (intensity < 0):
intensity = abs(intensity)
try:
calc_vis_elements.calc_vis_elements(
master, elements, seq_id, position, intensity, False,
True, False, anno_id, None, None)
except Exception:
print "ERROR", "RedrawStackedHeatmap", "Creating visualisation element failed for", seq_id, sys.exc_info(
)
position = position + 1
except Exception:
print "ERROR", "RedrawStackedHeatmap", sys.exc_info()
pass
position = position + 1
if (master.scale != None):
master.scale.destroy()
master.scale = None
if (master.button != None):
master.button.destroy()
master.button = None
def RedrawBarChart(master, loadSequences, _position=None, _seq=None, _set_ids=None, _elements=None, _heatMapSize=None, _ranges=None):
cur_window_size = -1
bin_start = None
bin_stop = None
if(len(master.SetIdList) > 0):
cur_shift_size = master.SetIdList[0].split("_")[2]
#master.button5["state"] = DISABLED
if( _position == None):
try:
master.root.canvas.delete('all')
except Exception:
pass
if(master.image_export_possible == True):
master.draw.rectangle((0, 0, master.image1Width, master.image1Height), fill="white")
master.lineChart = False
master.focusOnBarCharts = 1
if(_heatMapSize == None):
master.heatMapSize = 100
else:
master.heatMapSize = _heatMapSize
master.pswidth = 0
master.pswidthExport = 0
master.psheight = 0
barChart = {}
real_max = -1
if(_seq != None):
master.seq_ids = []
master.seq_ids.append(_seq)
if(_set_ids != None):
master.SetIdList = _set_ids
max_value = -1
max_value_total = -1
l = 0
if(len(master.SetIdList) > 0):
for seq in master.seq_ids:
if(_ranges != None and l < len(_ranges)):
bin_start = int(int(_ranges[l]) * 1000000)
master.bin_start = (bin_start / 1000000)
bin_stop = int(int(_ranges[l + 1]) * 1000000)
l = l + 2
counter = 0
elements_total = None
for value in master.SetIdList:
if(master.cmd_line == False):
master.display = "% bp"
elements = None
#master.NContent.set(100)
if(_elements == None):
elements = master.getElementsFromDatabase(seq, value, master.density_table, master.db_file, bin_start, bin_stop)[0]
if(master.display != "% bp"):
if(elements_total == None):
elements_total = [0] * (len(elements))
for i in range(0, len(elements)):
elements_total[i] = elements_total[i] + elements[i]
elements[i] = (elements[i])
else:
elements = _elements[value]
if(barChart.get(seq) == None):
barChart[seq] = {}
barChart[seq][counter] = []
barChart[seq][counter] = elements
if(master.colorToSetIdMap.get(value) != None):
master.colorMap[counter] = master.colorToSetIdMap.get(value)
else:
master.colorMap[counter] = master.colors[counter % len(master.colors)]
master.colorToSetIdMap[value] = master.colors[counter % len(master.colors)]
counter = counter + 1
if(master.cmd_line == True and master.display != "% bp"):
max_value = max(elements_total)
if(max_value_total < max_value):
max_value_total = max_value
real_max = max_value_total
if(master.cmd_line == True and master.display != "% bp"):
for seq in master.seq_ids:
amountElements = len((barChart.get(seq)).get(0))
for i in range(0, amountElements):
sum = 0
for k in range(0, len(barChart.get(seq).keys())):
barChart[seq].get(k)[i] = int((barChart[seq].get(k)[i] / float(real_max)) * 100.0)
position = 0
if(_position != None):
position = _position
x = 0
for seq in master.seq_ids:
if(_ranges != None and x < len(_ranges)):
bin_start = int(int(_ranges[x]) * 1000000)
master.bin_start = (bin_start / 1000000)
x = x + 2
amountElements = len((barChart.get(seq)).get(0))
for i in range(0, amountElements):
sum = 0
for k in range(1, len(barChart.get(seq).keys())):
barChart[seq].get(k)[i] += barChart[seq].get(k - 1)[i]
barChart[seq][counter] = []
master.colorMap[counter] = master.colorBackGround
for l in range(0, amountElements):
barChart.get(seq).get(counter).append(100)
keys = []
keys = barChart[seq].keys()
keys.reverse()
master.AdaptMaxLabelSize()
for ckey in keys:
if(len(seq) * master.fontSize > master.maxLabelSize):
master.maxLabelSize = len(seq) * master.fontSize
elements = barChart.get(seq).get(ckey)
for i in range(0, len(elements)):
elements[i] = elements[i] * master.heatMapSize / 100.0
calc_vis_elements.calc_vis_elements(master, elements , seq, position, 1, True, False, master.colorMap.get(ckey), "", None, None, real_max)
position = position + 1
if(_position != None):
return
calc_vis_elements.createBarChartLegend(master, "BarChart")
master.ChangeSize()
if(master.scale != None):
master.scale.destroy()
master.scale = None
if(master.button != None):
master.button.destroy()
master.button = None
def RedrawHeatmap(master, _ranges=None) :
try:
master.root.canvas.delete('all')
except Exception:
pass
if(master.image_export_possible == True):
master.draw.rectangle((0, 0, master.image1Width, master.image1Height), fill="white")
bin_start = None
bin_stop = None
master.heatMapSize = 75
master.focusOnBarCharts = 0
position = 1
mode = master.display
master.pswidth = 0
master.pswidthExport = 0
master.AdaptMaxLabelSize()
try:
master.getMax2()
except Exception:
pass
absolute_max = master.maxV
absolute_min = master.minV
try:
master.scale["to"] = math.ceil(absolute_max)
master.scale["from"] = math.ceil(absolute_min)
except Exception:
pass
l = 0
for seq_id in master.seq_ids:
elements = []
if(_ranges != None and l < len(_ranges)):
bin_start = int(int(_ranges[l]) * 1000000)
master.bin_start = (bin_start / 1000000)
bin_stop = int(int(_ranges[l + 1]) * 1000000)
l = l + 2
if(master.elementList.get(seq_id) == None or _ranges != None):
elements = master.getElementsFromDatabase(seq_id, master.set_id_A, master.density_table, master.db_file, bin_start, bin_stop)[0]
master.elementList[seq_id] = elements
else:
elements = master.elementList.get(seq_id)
try:
scaleValue = master.scale.get()
if(scaleValue == 0):
scaleValue = master.maxV
except Exception:
scaleValue = master.maxV
#SCALING PARAMETER
scaleValue = 100 #damit heatmap colors zw. 0 und 100 prozent skaliert
if(scaleValue - absolute_min == 0):
intensityF = absolute_max / absolute_min
elif(scaleValue - absolute_min < 0):
intensityF = 0
else:
intensityF = (absolute_max - absolute_min) / (scaleValue - absolute_min)
calc_vis_elements.calc_vis_elements(master, elements, seq_id, position, intensityF, False, False, False, "", absolute_min, absolute_max, None)
position = position + 1
if len(master.seq_ids) > 0:
calc_vis_elements.createColorMap(master, mode)
def RedrawStackedHeatmap(master, heatMapSize=None, _ranges=None):
try:
master.button5["state"] = NORMAL
master.root.canvas.delete('all')
if(master.image_export_possible == True):
master.draw.rectangle((0, 0, master.image1Width, master.image1Height), fill="white")
except Exception:
pass
master.lineChart = False
master.pswidth = 0
master.psheight = 0
master.gapBetweenHeatmaps = 0
if(heatMapSize == None):
master.heatMapSize = 50
else:
master.heatMapSize = heatMapSize
position = 0
master.focusOnBarCharts = 2
seq_ids = master.seq_ids
anno_ids = master.anno_ids
master.AdaptMaxLabelSize()
l = 0
bin_start = None
bin_stop = None
for seq_id in seq_ids:
if(_ranges != None and l < len(_ranges)):
bin_start = int(int(_ranges[l]) * 1000000)
bin_stop = int(int(_ranges[l + 1]) * 1000000)
l = l + 2
for anno_id in anno_ids:
master.set_id_A = anno_id
try:
minIntensity = None
maxIntensity = None
try:
master.calculateMinAndMax()
print "anno_id::",anno_id,seq_id
minIntensity = master.anno_ids_mItensities[anno_id]["min"]
maxIntensity = master.anno_ids_mItensities[anno_id]["max"]
print "max:",maxIntensity,"min:",minIntensity
print "\n\n";
except Exception:
print "ERROR", "RedrawStackedHeatmap", sys.exc_info()
cIntensity = None
filterOn=False
try:
cIntensity = master.anno_ids_mItensities[seq_id]["cur"]
print "INFO", "using seq_id constraint", cIntensity, "for seq_id", seq_id
filterOn=True
except Exception:
pass
try:
cIntensity = master.anno_ids_mItensities[anno_id]["cur"]
print "INFO", "using set_id constraint", cIntensity, "for set_id", anno_id
filterOn=True
except Exception:
pass
try:
cIntensity = master.anno_ids_mItensities[seq_id+"_"+anno_id]["cur"]
filterOn=True
print "INFO", "using seq_id+set_id constraint", cIntensity, "for set_id", anno_id
except Exception:
pass
#
elements = master.getElementsFromDatabase(seq_id, anno_id, master.density_table, master.db_file, bin_start, bin_stop)[0]
#
if(cIntensity == None):
print "INFO", "cIntensity>maxIntensity",maxIntensity
cIntensity = maxIntensity
elif(int(cIntensity) == -1):
print "INFO", "using track max",max(elements)
cIntensity = max(elements)
#
if(filterOn==True):
intensity = max(elements)/cIntensity
else:
intensity = max(elements)/maxIntensity
#
if(intensity < 0):
intensity = abs(intensity)
try:
calc_vis_elements.calc_vis_elements(master, elements, seq_id, position, intensity , False, True, False, anno_id, None, None)
except Exception:
print "ERROR", "RedrawStackedHeatmap", "Creating visualisation element failed for", seq_id, sys.exc_info()
position = position + 1
except Exception:
print "ERROR", "RedrawStackedHeatmap", sys.exc_info()
pass
position = position + 1
if(master.scale != None):
master.scale.destroy()
master.scale = None
if(master.button != None):
master.button.destroy()
master.button = None
