def draw_figure(canvas, figure, canvas_toolbar):
if canvas.children:
for child in canvas.winfo_children():
child.destroy()
if canvas_toolbar.children:
for child in canvas_toolbar.winfo_children():
child.destroy()
figure_canvas_agg = FigureCanvasTkAgg(figure, canvas)
figure_canvas_agg.draw()
toolbar = Toolbar(figure_canvas_agg, canvas_toolbar)
toolbar.config(background='#E3B04B',)
for button in toolbar.winfo_children():
button.config(background='#E3B04B')
toolbar.update()
figure_canvas_agg.get_tk_widget().pack(side="top", fill="both", expand=1)
class CustomDialog(Dialog):
def __init__(self, parent, title, components):
if not parent:
parent = tkinter._default_root
self.results = None
self.components = components
Dialog.__init__(self, parent, title)
def destroy(self):
self.components = None
Dialog.destroy(self)
def body(self, master):
first_entry = None
row = 0
grid_frame = tkinter.Frame(master) # Form
plot_frame = tkinter.Frame(master) # Plot
stats_frame = tkinter.Frame(master) # Listbox
for i, component in enumerate(self.components):
row += i
if component["type"].lower() == "label":
component["object"] = tkinter.Label(grid_frame, text=component["text"])
component["object"].grid(row=row, columnspan=2)
if component["type"].lower() == "entry":
tkinter.Label(grid_frame, text=component["text"]).grid(row=row, sticky=tkinter.W)
component["object"] = tkinter.Entry(grid_frame, justify=tkinter.RIGHT)
component["object"].delete(0, tkinter.END)
component["object"].insert(0, str(component["default"]))
component["object"].grid(row=row, column=1)
if first_entry is None:
first_entry = component["object"]
elif component["type"].lower() == "checkbutton":
component["variable"] = tkinter.IntVar() # set to 1 if the button is selected, and 0 otherwise
component["variable"].set(component["default"])
component["object"] = tkinter.Checkbutton(grid_frame, text=component["text"], variable=component["variable"])
component["object"].grid(row=row, columnspan=2, sticky=tkinter.E)
#elif component["type"].lower() == "combobox":
elif component["type"].lower() == "optionmenu":
if len(component["options"]) <= 0:
raise Exception("Options needed!")
tkinter.Label(grid_frame, text=component["text"]).grid(row=row, sticky=tkinter.W)
component["variable"] = tkinter.StringVar()
if "ttk" in list(sys.modules.keys()):
# It supports better long lists of options
max_width = 20
for value in component["options"]:
if len(value) > max_width:
max_width = len(value)+1
component["variable"].set(component["default"])
component["object"] = tkinter.ttk.Combobox(grid_frame, textvariable=component["variable"], state='readonly', width=max_width)
component["object"]['values'] = tuple(component["options"])
component["object"].grid(row=row, column=1, sticky=tkinter.W)
else:
tkinter.Label(grid_frame, text=component["text"]).grid(row=row, sticky=tkinter.W)
component["variable"] = tkinter.StringVar()
component["variable"].set(component["default"])
component["object"] = tkinter.OptionMenu(*(grid_frame, component["variable"]) + tuple(component["options"]))
component["object"].grid(row=row, column=1, sticky=tkinter.W)
elif component["type"].lower() == "radiobutton":
tkinter.Label(grid_frame, text=component["text"]).grid(row=row, sticky=tkinter.W)
component["variable"] = tkinter.StringVar()
objects = []
for j, text in enumerate(component["options"]):
objects.append(tkinter.Radiobutton(grid_frame, text=text, variable=component["variable"], value=text))
objects[-1].grid(row=row, column=1, sticky=tkinter.W)
row += 1
component["variable"].set(component["default"])
elif component["type"].lower() == "listbox" and component["options"] is not None and len(component["options"]) > 0:
stats_scrollbar = tkinter.Scrollbar(stats_frame, orient=tkinter.VERTICAL)
component["object"] = tkinter.Listbox(stats_frame, height=5, yscrollcommand=stats_scrollbar.set, font=('courier',10,'normal'), selectmode=tkinter.EXTENDED)
stats_scrollbar.pack(side=tkinter.RIGHT, fill=tkinter.Y)
component["object"].delete(0, tkinter.END) # Delete all
for text in component["options"]:
component["object"].insert(tkinter.END, text)
component["object"].pack(fill=tkinter.BOTH, expand=1)
elif component["type"].lower() == "plot" and component["function"] is not None:
# Create the mpl Figure and FigCanvas objects.
# 5x4 inches, 100 dots-per-inch
#
self.dpi = 100
self.fig = Figure((6.0, 3.0), dpi=self.dpi)
self.canvas = FigCanvas(self.fig, master=plot_frame)
self.canvas.draw()
#self.canvas.get_tk_widget().grid(row = 0, column = 0) # or .grid(row = 0)
### Since we have only one plot, we can use add_axes
### instead of add_subplot, but then the subplot
### configuration tool in the navigation toolbar wouldn't
### work.
###
if component["axes"] == 1:
self.axes = self.fig.add_subplot(1, 1, 1)
#### Avoid using special notation that are not easy to understand in axis for big zoom
myyfmt = ScalarFormatter(useOffset=False)
self.axes.get_xaxis().set_major_formatter(myyfmt)
self.axes.get_yaxis().set_major_formatter(myyfmt)
self.toolbar = NavigationToolbar(self.canvas, plot_frame)
self.toolbar.update()
self.canvas._tkcanvas.pack(side=tkinter.TOP, fill=tkinter.BOTH, expand=1)
elif component["axes"] > 1:
self.axes = []
for i in range(component["axes"]):
self.axes.append(self.fig.add_subplot(2, 1, i+1))
#### Avoid using special notation that are not easy to understand in axis for big zoom
myyfmt = ScalarFormatter(useOffset=False)
self.axes[i].get_xaxis().set_major_formatter(myyfmt)
self.axes[i].get_yaxis().set_major_formatter(myyfmt)
self.toolbar = NavigationToolbar(self.canvas, plot_frame)
self.toolbar.update()
self.canvas._tkcanvas.pack(side=tkinter.TOP, fill=tkinter.BOTH, expand=1)
# Plotting function
component["function"](*(self.axes, component))
plot_frame.pack(side=tkinter.TOP, fill=tkinter.BOTH, expand=1)
stats_frame.pack(side=tkinter.TOP, fill=tkinter.BOTH, expand=1)
grid_frame.pack(side=tkinter.TOP, fill=tkinter.BOTH, expand=1)
# Which should receive focus:
return first_entry
def validate(self):
for component in self.components:
if component["type"] == "Entry":
try:
#value = float(component["object"].get())
if component["text-type"] == "str":
value = eval(component["text-type"] + "('%s')" % component["object"].get())
else:
value = eval(component["text-type"] + "(%s)" % component["object"].get())
except Exception:
tkinter.messagebox.showwarning(
"Illegal value",
"Illegal value for " + component["text"] + "\nPlease try again",
parent = self
)
return 0
if component["minvalue"] is not None and value < component["minvalue"]:
tkinter.messagebox.showwarning(
"Too small",
"'%s': "
"The allowed minimum value is %s. "
"Please try again." % (component["text"], component["minvalue"]),
parent = self
)
return 0
if component["maxvalue"] is not None and value > component["maxvalue"]:
tkinter.messagebox.showwarning(
"Too big",
"'%s': "
"The allowed maximum value is %s. "
"Please try again." % (component["text"], component["maxvalue"]),
parent = self
)
return 0
return 1
def apply(self):
self.results = {}
for component in self.components:
# Save results and modify defaults
if component["type"] == "Entry":
if component["text-type"] == "str":
value = eval(component["text-type"] + "('%s')" % component["object"].get())
else:
value = eval(component["text-type"] + "(%s)" % component["object"].get())
self.results[component["text"]] = value
component["default"] = str(value)
elif component["type"] in ["Checkbutton", "OptionMenu", "Radiobutton"]:
self.results[component["text"]] = component["variable"].get()
component["default"] = component["variable"].get()
def itemClicked(event):
specKey = str(left_tree.focus())
global f, f2, canvas, specCanvas, onlySpectra, threeDthing, spectrumWindow, lineCollection, redlineCollection, ax, allSpecPreviousExistence, allSpectra, allLines
print(specKey)
chromKey = specKey.split("|")[0]
if allSpecPreviousExistence is not chromKey:
if len(lineCollection) > 0:
for specNum in list(lineCollection):
#for aLine in lineCollection[specNum]:
# aLine.remove()
del lineCollection[specNum]
del redlineCollection[:]
f2.clf()
# all spectra 3D plot------------------------------------------------
if spectrumWindow.winfo_exists() == 0:
spectrumWindow = Tk.Toplevel() # Makes the window
spectrumWindow.wm_title("All Spectra")
spectrumWindow.geometry("700x650")
topFrame = Tk.Frame(spectrumWindow, width=700, height=700)
topFrame.pack(side="top", fill="both", expand=True)
specCanvas = FigureCanvasTkAgg(f2, master=topFrame)
specCanvas.get_tk_widget().pack(side="top",
fill="both",
expand=True)
theTool2 = PlotNav(specCanvas, topFrame)
theTool2.update()
# on demand loading of all spectral data---------------------------------------
if chromKey not in allSpectra:
allSpectra[chromKey] = []
clustData = next(
iter(os.walk(os.path.join(allMSdataPath, chromKey))))
#print os.path.join(allMSdataPath, chromKey)
clusterPath = os.path.join(allMSdataPath, chromKey)
majSpecBool = False
internalSpecCount = 1
for filename in clustData[2]:
#print filename
if ((".txt" in filename) & ("_" in filename)):
spectrumReader = open(os.path.join(clusterPath, filename),
"r")
_textOut = ""
_spectrum = []
_count = 0
for line in spectrumReader:
#_textOut += line
if _count == 0:
_precursor = float(
re.search(r'\d+\.\d+', line).group())
_textOut += line
elif _count == 1:
_intensity = float(
re.search(r'\d+\.\d+', line).group())
_textOut += line
elif _count == 2:
_charge = int(re.search(r'\d', line).group())
_textOut += line
elif _count == 3:
_rt = float(re.search(r'\d+\.\d+', line).group())
_textOut += line
elif _count == 4:
_scanNo = float(re.search(r'\d+', line).group())
_textOut += line
elif _count == 6:
_id = re.search(filenamePatt, line).group(1)
_textOut += line
else:
spectrumData = re.match(spectrumPatt, line)
if spectrumData != None:
_spectrum.append([
float(spectrumData.group(1)),
float(spectrumData.group(2))
])
#_textOut += theMZ + " " + str(round(theAb, 2))
else:
_textOut += line
_count += 1
spectrumReader.close()
storedMSdata[chromKey][1].append(
[_precursor, _charge, _rt, internalSpecCount])
chromLoc[chromKey][0].append(_rt)
chromLoc[chromKey][1].append(_precursor)
chromLoc[chromKey][2].append(_intensity)
chromLoc[chromKey][3].append("S%s" % (internalSpecCount))
chromLoc[chromKey][4].append(_id)
numRows = int(math.ceil(len(_spectrum) / 6.0))
_specOut = ["" for i in range(numRows)]
for i, peak in enumerate(_spectrum):
strMZ = str(peak[0])
strAb = str(round(peak[1], 2))
_specOut[i % numRows] += strMZ + " " + strAb + "\t\t\t"
_specOut.insert(
0, "\n" + "m/z\tAbundance\t\t" * 6 + "\n" +
"-------------------------------\t\t\t" * 6)
for aline in _specOut:
_textOut += aline + "\n"
onlySpectra[chromKey + "|" + str(internalSpecCount)] = [
_precursor, _charge, _rt, _spectrum, _textOut,
internalSpecCount
]
allSpectra[chromKey].append([_spectrum, internalSpecCount])
internalSpecCount += 1
if "majority" in filename:
majSpecBool = True
majSpectrumReader = open(
os.path.join(clusterPath, filename), "r")
_textOut = ""
_spectrum = []
_count = 0
for line in majSpectrumReader:
#_textOut += line
if _count == 0:
_monoIso = float(
re.search(r'\d+\.\d+', line).group())
_textOut += line
elif _count == 1:
if "UNKNOWN" not in line:
_charge = int(re.search(r'\d', line).group())
else:
_charge = 0
_textOut += line
elif _count == 2:
_constituentCount = int(
re.search(r'\d+', line).group())
_textOut += line
else:
majspectrumData = re.match(majSpectrumPatt, line)
if majspectrumData is not None:
_spectrum.append([
float(majspectrumData.group(1)),
float(majspectrumData.group(2)),
majspectrumData.group(3)
])
#_textOut += theMZ + " " + str(round(theAb, 2))
else:
_textOut += line
_count += 1
majSpectrumReader.close()
numRows = int(math.ceil(len(_spectrum) / 5.0))
_specOut = ["" for i in range(numRows)]
_maxMZmaj = max(_spectrum)[0]
_minMZmaj = min(_spectrum)[0]
for i, peak in enumerate(_spectrum):
strMZ = str(peak[0])
strAb = str(round(peak[1], 2))
if len(strAb) > 5:
strAb = str(round(peak[1], 1))
anno = peak[2]
_specOut[
i %
numRows] += strMZ + " " + strAb + "\t" + anno + "\t\t\t"
_specOut.insert(
0, "\n" + "m/z\tAb Freq Error\t\t\t" * 5 + "\n" +
"---------------------------------------\t\t\t\t" * 5)
for aline in _specOut:
_textOut += aline + "\n"
onlySpectra[chromKey + "|Majority"] = [
_monoIso, _charge, "N/A", _spectrum, _textOut,
"Majority", _maxMZmaj, _minMZmaj
]
# add to the tree!
if majSpecBool:
left_tree.insert(chromKey,
"end",
chromKey + "|Majority",
text="MajoritySpectrum",
values=("", "", _monoIso, "N/A"))
for spectrumData in storedMSdata[chromKey][1]:
spectrumCount = spectrumData[3]
specTreeName = chromKey + "|" + str(spectrumCount)
_prec = spectrumData[0]
_rt = spectrumData[2]
left_tree.insert(chromKey,
"end",
specTreeName,
text="Spectrum" + str(spectrumCount),
values=("", "", _prec, _rt))
# ------------------ on demand chromatographic data loading
chromReader = open(
os.path.join(clusterPath, "chromatographicData.csv"), "r")
firstLine = chromReader.readline().rstrip()
chromReader.readline()
_chromStats = []
for line in chromReader:
if "enter: " in line:
_initialInfo = line.rstrip()
_precursorChrom = float(
re.search(precursorPatt, _initialInfo).group(1))
_identifier = re.search(filenamePatt,
_initialInfo).group(1)
elif "Retention" in line:
_isoMZs = [
float(isoMZ) for isoMZ in re.findall(isoMZPatt, line)
]
else:
chromData = re.match(chromPatt, line)
if chromData != None:
theAbs = re.findall(AbPatt, line)
_chromStats.append(
[float(chromData.group(1))] +
[float(abVal[1:]) for abVal in theAbs])
if line.rstrip() == "":
#storedMSdata[chromKey]["chromData"].append([_initialInfo, _precursorChrom, _chromStats])
_sortedChromStats = sorted(_chromStats)
onlyChrom[chromKey][0].add(_identifier)
onlyChrom[chromKey][1].append([
_initialInfo, _precursorChrom, _sortedChromStats,
_identifier, _isoMZs
])
_chromStats = []
_initialInfo = ""
_precursorChrom = "WRONG"
#if len(storedMSdata[chromKey]["chromData"]) > 1:
# print storedMSdata[chromKey]["chromData"]
chromReader.close()
#----------------------------------------------------------- 3D drawing of all spectra in the cluster
allTheSpectra = allSpectra[chromKey]
#if len(allTheSpectra) > 1:
ax = f2.add_subplot(111, projection='3d')
f2.subplots_adjust(left=0.02,
right=0.98,
top=0.98,
bottom=0.02,
wspace=0.02)
ax.set_xlabel('m/z')
ax.set_ylabel('Spectrum Index')
ax.set_zlabel('Intensity')
allMZ = []
allIndex = []
for threedspec in allTheSpectra:
theSpectrum = threedspec[0]
_theIndex = threedspec[1]
lineCollection[_theIndex] = []
allIndex.append(_theIndex)
for peak in theSpectrum:
_theMZ = peak[0]
_theAbs = peak[1]
if _theAbs > 50:
line = art3d.Line3D(*zip((_theMZ, _theIndex, 0),
(_theMZ, _theIndex, _theAbs)),
marker=' ',
markevery=(1, 1))
ax.add_line(line)
lineCollection[_theIndex].append(line)
allMZ.append(_theMZ)
ax.set_xlim(min(allMZ), max(allMZ))
ax.set_ylim(0, len(allTheSpectra) + 1)
ax.set_yticks(allIndex)
ax.set_zlim(0, 1100)
toolbar2 = f2.canvas.toolbar
toolbar2.update()
specCanvas.draw()
allSpecPreviousExistence = chromKey
# ------------------------------- 2D spectrum viewer
if specKey in onlySpectra:
#plt.clf()
if len(threeDthing) > 0:
a3dthing = threeDthing.pop()
f.delaxes(a3dthing)
#a3dthing.remove()
del a3dthing
#a = f.add_subplot(111)
a = f.add_subplot(111)
f.subplots_adjust(left=0.06, right=0.94, top=0.9, bottom=0.1)
a.stem([0], [0], markerfmt=' ')
a.spines['top'].set_visible(False)
a.spines['right'].set_visible(False)
#print specKey
precursorMZ = onlySpectra[specKey][0]
filteredSpectrum = onlySpectra[specKey][3]
textOut = onlySpectra[specKey][4]
specNum = onlySpectra[specKey][5]
localMajorityBool = False
if chromKey + "|Majority" in onlySpectra:
localMajorityBool = True
majMZmax = onlySpectra[chromKey + "|Majority"][6]
majMZmin = onlySpectra[chromKey + "|Majority"][7]
if len(redlineCollection) > 0:
previousSpecNum = redlineCollection[0][1][1]
for aLine in lineCollection[previousSpecNum]:
ax.add_line(aLine)
[rLine[0].remove() for rLine in redlineCollection]
redlineCollection = []
if specNum != "Majority":
for aLine in lineCollection[specNum]:
aLine.remove()
sortedSpectrum = sorted(filteredSpectrum)
xData = []
yData = []
for anAttr in sortedSpectrum:
xData.append(anAttr[0])
yData.append(anAttr[1] / 10)
if localMajorityBool is False:
theRange = (max(xData) + 10) - (min(xData) - 10)
a.set_xlim(min(xData) - 10, max(xData) + 10)
else:
theRange = (majMZmax + 10) - (majMZmin - 10)
a.set_xlim(majMZmin - 10, majMZmax + 10)
print("worked!")
a.arrow(float(precursorMZ),
3,
0.0,
-1,
fc="k",
ec="k",
head_width=theRange * 0.01,
head_length=2)
a.stem(xData, yData, 'silver', markerfmt=' ')
a.set_ylim(0, 110)
a.axvline(0, color='black', linewidth=2)
a.grid(color='lightgray', alpha=0.7)
a.set_xlabel("m/z", fontsize=12)
a.set_ylabel("Relative Intensity", fontsize=12)
whatToPlot = []
theRecords = [
] # you use this to check if there is any peak that is in the range of your current peak that would get in the way of the text (i.e. it's a higher intensity)
for mz_intensity in sortedSpectrum:
#this code will only allow text to be plotted either if the preceding plotted text is far enough away ( > theRange*0.05), or if it has a higher intensity than the preceding plotted text (which it subsequently removes)
originalIntensity = mz_intensity[1]
_xcoor = mz_intensity[0]
_ycoor = originalIntensity / 10.0
if ((originalIntensity > 50) & (specNum != "Majority")):
line = art3d.Line3D(*zip((_xcoor, specNum, 0),
(_xcoor, specNum, originalIntensity)),
marker=' ',
c='r',
markevery=(1, 1))
ax.add_line(line)
redlineCollection.append(
[line, (_xcoor, specNum, originalIntensity)])
if len(whatToPlot) > 0:
last_xcoor = whatToPlot[-1][0]
last_ycoor = whatToPlot[-1][1]
#print "%s --> %s" % (_xcoor, _xcoor - last_xcoor)
if (_xcoor - last_xcoor < theRange * 0.05) & (
_ycoor > last_ycoor
) & (
_ycoor > 1
): # if it is NOT far enough away BUT it is taller than the last text then go ahead
whatToPlot.pop()
whatToPlot.append([_xcoor, _ycoor])
#print "popped! %s" % (last_xcoor)
elif (_xcoor - last_xcoor > theRange * 0.05) & (
_ycoor > 1
): # if it is far enough away from the last text then go ahead
goAhead = True
for checkPrevious in theRecords:
if (_xcoor - checkPrevious[0] < theRange * 0.05) & (
_ycoor < checkPrevious[1]
): # check to see if anything in range that is also greater than the current intensity
goAhead = False
if goAhead == True: whatToPlot.append([_xcoor, _ycoor])
else:
if (_ycoor > 1): whatToPlot.append([_xcoor, _ycoor])
theRecords.append([_xcoor, _ycoor])
#a.arrow(float(precursorMZ), 3, 0.0, -1, fc="k", ec="k", head_width=theRange*0.05, head_length=5)
for dataToPlot in whatToPlot:
a.annotate(str(dataToPlot[0]),
xy=(dataToPlot[0], dataToPlot[1]),
ha='center',
size='x-small')
toolbar1 = f.canvas.toolbar
toolbar1.update()
canvas.draw()
toolbar2 = f2.canvas.toolbar
toolbar2.update()
specCanvas.draw()
threeDthing.append(a)
specData.delete(1.0, Tk.END)
specData.insert(0.0, textOut)
# ------------------------------- MS1 chromatogram plot
elif specKey in onlyChrom:
if len(threeDthing) > 0:
a3dthing = threeDthing.pop()
f.delaxes(a3dthing)
#a3dthing.remove()
del a3dthing
f.clf()
ax2 = f.add_subplot(111, projection='3d')
ax2.set_xlabel('retention time (seconds)')
ax2.set_ylabel('m/z')
ax2.set_zlabel('Raw Abundance')
IDset = onlyChrom[specKey][0]
fileNames = dict([(_id, (i * 0.01, i))
for i, _id in enumerate(sorted(IDset))])
allLines = dict([(_id, []) for _id in IDset])
#print fileNames
theData = onlyChrom[specKey][1]
specLocations = chromLoc[specKey]
allMZs = []
textOut = onlyChrom[specKey][2] + "\n\n"
#print theData
#allTrueTraceMZs = set([math.floor(aSet[1]*10) for aSet in theData])
allTrueTraceMZs = dict([(_id, set()) for _id in IDset])
for aSet in theData:
_identifier = aSet[3]
quickSearchVal = round(aSet[1] * 10)
allTrueTraceMZs[_identifier].add(quickSearchVal)
#print allTrueTraceMZs
for aSet in theData:
setLines = []
_readOutData = aSet[0]
textOut += _readOutData + "\n"
_identifier = aSet[3]
_isoMZs = aSet[4]
theOffset = fileNames[_identifier][0]
#theOffset = 0
colorIndex = fileNames[_identifier][1]
theLength = len(aSet[2])
_prec = [aSet[1] for i in range(theLength)]
_rt = [aSet[2][i][0] for i in range(theLength)]
_real = [aSet[2][i][1] for i in range(theLength)]
setLines = []
#print(aSet[2])
if len(aSet[2][0]) > 2:
_fitted = [aSet[2][i][2] for i in range(theLength)]
theLineFitted, = ax2.plot(_rt,
_prec,
_fitted,
c='mediumblue',
linestyle='--',
label=_identifier)
setLines.append(theLineFitted)
# remember this HAS to come AFTER the fitted gaussian line because the legend color will be all messed up
theLineReal, = ax2.plot(_rt,
_prec,
_real,
c=colors[colorIndex % len(colors)],
label=_identifier)
setLines.append(theLineReal)
allMZs.extend(_prec)
for i, isoMZ in enumerate(_isoMZs):
if round(isoMZ * 10) not in allTrueTraceMZs[_identifier]:
_isoTrace = [aSet[2][j][i + 3] for j in range(theLength)]
_isoPrec = [isoMZ for i in range(theLength)]
ghostLine, = ax2.plot(_rt,
_isoPrec,
_isoTrace,
c=colors[colorIndex % len(colors)],
label=_identifier,
linestyle=':')
allMZs.extend(_isoPrec)
setLines.append(ghostLine)
allLines[_identifier].extend(setLines)
handles, labels = ax2.get_legend_handles_labels()
by_label = OrderedDict(zip(labels, handles))
#theLeg = ax2.legend(list(by_label.values()), list(by_label), loc=2, prop={'size': 7}, bbox_to_anchor=(1, 1)) # remember this moves the legend to not overlap the graph
theLeg = ax2.legend(by_label.values(),
by_label.keys(),
loc=2,
prop={'size': 9})
#modYcoors = []
for x, y, z, theLabel, _id in zip(specLocations[0], specLocations[1],
specLocations[2], specLocations[3],
specLocations[4]):
theOffset = fileNames[_id][0]
colorIndex = fileNames[_id][1]
theText = ax2.text(x, y, z, theLabel, size=9, color='k', label=_id)
#modYcoors.append(y+theOffset)
theScat = ax2.scatter(x,
y,
z,
c=colors[colorIndex % len(colors)],
marker='.',
s=40,
label=_id)
allLines[_id].extend([theText, theScat])
[legline.set_picker(5)
for legline in theLeg.get_lines()] # 5 pts tolerance
minMZ = min(allMZs + specLocations[1]) - 0.05
maxMZ = max(allMZs + specLocations[1]) + 0.05
ax2.set_ylim(minMZ, maxMZ)
threeDthing.append(ax2)
specData.delete(1.0, Tk.END)
specData.insert(0.0, textOut)
#ax2.legend(loc=2, prop={'size': 9})
#ax.set_axis_off
#ax.scatter(pc1[ctrlN:], pc2[ctrlN:], pc3[ctrlN:], c='b', marker='^',s=60)
canvas.mpl_connect('pick_event', onpick)
canvas.mpl_connect('button_press_event',
lambda event: canvas._tkcanvas.focus_set())
canvas.mpl_connect('key_press_event', on_key_press)
canvas.draw()
#rightFrame.grid(row=0, column=1, padx=10, pady=2)
specData = Tk.Text(rightFrame,
width=160,
height=20,
takefocus=0,
font=customFont)
#specData.grid(row=4, column=0, padx=10, pady=2)
specData.pack(side="bottom", in_=rightFrame, fill="both", expand=True)
canvas = FigureCanvasTkAgg(f, master=rightFrame)
canvas.get_tk_widget().pack(side="top", fill="both")
theTool = PlotNav(canvas, rightFrame)
theTool.update()
canvas.draw()
topFrame = Tk.Frame(spectrumWindow, width=700, height=700)
topFrame.pack(side="top", fill="both", expand=True)
specCanvas = FigureCanvasTkAgg(f2, master=topFrame)
specCanvas.get_tk_widget().pack(side="top", fill="both", expand=True)
theTool2 = PlotNav(specCanvas, topFrame)
theTool2.update()
specCanvas.draw()
#canvas.get_tk_widget().grid(column=0,row=1)
#canvas.get_tk_widget().pack_forget()