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mzmlplot.py

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+import os
+import sys
+from PyQt6 import uic
+from PyQt6.QtGui import *
+from PyQt6.QtCore import pyqtSlot, Qt, pyqtSignal
+from PyQt6.QtWidgets import *
+from PyQt6.uic import loadUi
+import pyopenms as oms
+import matplotlib.pyplot as plt
+import matplotlib.ticker as ticker
+import pandas as pd
+from mzmlplot_ui import Ui_MainWindow
+
+
+
+class MainWindow(QMainWindow):
+    def __init__ (self):
+        super().__init__()
+        self.ui = Ui_MainWindow()
+        self.ui.setupUi(self)
+        self.ui.fileselectButton.clicked.connect(self.file_finder)
+        self.ui.plotButton.clicked.connect(self.plot)
+        self.show()
+
+    def extract_intensity(self, spectrum, mz_value):
+        try:
+            #Peak pick for closest peak to desired m/z value
+            closest_peak = min(spectrum, key=lambda x: abs(x.getMZ() - mz_value))
+            #return intensity of the closest peak
+            return closest_peak.getIntensity()
+        except ValueError: #if a peak is not present, an empty line will be added to the dataframe
+            return None
+
+    def file_finder(self):
+        #User input for input file location - must be mzml currently
+        file_dialog_result = QFileDialog.getOpenFileName()
+        selected_file_path = file_dialog_result[0]
+
+        if selected_file_path:
+            self.ui.fileLineedit.setText(selected_file_path)
+
+    def plot(self):
+        modeboxindex = self.ui.modeBox.currentIndex()
+        if modeboxindex == 0:
+            self.plotsinglescan()
+        elif modeboxindex == 1:
+            self.plotmergedscans()
+        elif modeboxindex == 2:
+            self.plottic()
+        elif modeboxindex == 3:
+            self.ploteic()
+
+
+
+    def plotsinglescan(self):
+        file = self.ui.fileLineedit.text()
+        #create an MSExperiment object to load the mzml file into
+        inp = oms.MSExperiment()
+        oms.MzMLFile().load(file, inp)
+
+        #In the square brackets, type the scan number you want to view
+        scan = [self.ui.scannumberSpinbox.value()]
+
+        #Create a new MSExperiment object to extract the scan to
+        filtered = oms.MSExperiment()
+
+        #Add the selected scan to the filtered MSExperiment object
+        for k, s in enumerate(inp):
+            if k in scan:
+                filtered.addSpectrum(s)
+
+        #Set up the plot window - not too important as it can be resized at will when open
+        fig, axs = plt.subplots(1)
+        fig.set_figheight(4)
+        plt.subplots_adjust(hspace=1)
+
+        #setup the axis params for the figure
+        s = filtered[0]
+
+        #If you are using profile data, keep this as 'axs.plot'. If using centroid, change to 'axs.stem' and delete ', linewidth = x'
+        #You can change the line colour here by changing the colour name in " ", and also change the line thickness
+        if self.ui.profileButton.isChecked():
+            axs.plot(s.get_peaks()[0],s.get_peaks()[1], self.ui.colourBox.currentText(), linewidth = self.ui.widthBox.value())
+        elif self.ui.centroidButton.isChecked():
+            markerline, stemlines, baseline = axs.stem(s.get_peaks()[0],s.get_peaks()[1], self.ui.colourBox.currentText(), markerfmt='none')
+            plt.setp(stemlines, 'linewidth', self.ui.widthBox.value())
+
+        #set the y-axis upper and lower limits - accepts raw integers or scientific notation
+        axs.set_ylim(self.ui.lowySpinbox.value(), self.ui.highySpinbox.value())
+
+        #Set the x-axis upper and lower limit - accepts raw integers or scientific notation
+        axs.set_xlim(self.ui.lowxSpinbox.value(), self.ui.highxSpinbox.value())
+
+        #Sets the x/y-axis labels
+        axs.set_xlabel("m/z")
+        axs.set_ylabel("Counts")
+
+        #sets the y-axis tick labels to scientific notation
+        axs.yaxis.set_major_formatter(ticker.FormatStrFormatter('%0.0e'))
+
+        #sets the figure to a tight layout
+        fig.tight_layout()
+
+        #shows the figure where you can zoom/resize at will, and save to a file (recommended to save as a .svg for figure scaling)
+        plt.show()
+
+    def plotmergedscans(self):
+        file = self.ui.fileLineedit.text()
+
+        # load MS data and store as MSExperiment object
+        exp = oms.MSExperiment()
+        oms.MzMLFile().load(file, exp)
+
+        spectra = exp.getSpectra()
+
+        # Collecting only MS1 spectra
+        spectra_ms1 = [s for s in spectra if s.getMSLevel() == 1]
+        print(f"Number of MS1 spectra before merge are {len(spectra_ms1)}")
+
+        # merges blocks of MS1
+        merger = oms.SpectraMerger()
+        merger.mergeSpectraBlockWise(exp)
+        param = merger.getParameters()
+        param.setValue("block_method:rt_block_size", len(exp.getSpectra()))
+        merger.setParameters(param)
+        merger.mergeSpectraBlockWise(exp)
+
+        # adjust block size to 10 spectra and merge
+        merger = oms.SpectraMerger()
+
+        param = merger.getParameters()
+        param.setValue("block_method:rt_block_size", len(exp.getSpectra()))
+        merger.setParameters(param)
+        merger.mergeSpectraBlockWise(exp)
+
+        spectraMerged = exp.getSpectra()
+        spectraMerged_ms1_10scans = [s for s in spectraMerged if s.getMSLevel() == 1]
+
+                #Set up the plot window - not too important as it can be resized at will when open
+        fig, axs = plt.subplots(1)
+        fig.set_figheight(4)
+        plt.subplots_adjust(hspace=1)
+
+        #setup the axis params for the figure
+        s = spectraMerged[0]
+
+        #If you are using profile data, keep this as 'axs.plot'. If using centroid, change to 'axs.stem' and delete ', linewidth = x'
+        #You can change the line colour here by changing the colour name in " ", and also change the line thickness
+        if self.ui.profileButton.isChecked():
+            axs.plot(s.get_peaks()[0],s.get_peaks()[1], self.ui.colourBox.currentText(), linewidth = self.ui.widthBox.value())
+        elif self.ui.centroidButton.isChecked():
+            markerline, stemlines, baseline = axs.stem(s.get_peaks()[0],s.get_peaks()[1], self.ui.colourBox.currentText(), markerfmt='none')
+            plt.setp(stemlines, 'linewidth', self.ui.widthBox.value())
+        #set the y-axis upper and lower limits - accepts raw integers or scientific notation
+        axs.set_ylim(self.ui.lowySpinbox.value(), self.ui.highySpinbox.value())
+
+        #Set the x-axis upper and lower limit - accepts raw integers or scientific notation
+        axs.set_xlim(self.ui.lowxSpinbox.value(), self.ui.highxSpinbox.value())
+
+        #Sets the x/y-axis labels
+        axs.set_xlabel("m/z")
+        axs.set_ylabel("Counts")
+
+        #sets the y-axis tick labels to scientific notation
+        axs.yaxis.set_major_formatter(ticker.FormatStrFormatter('%0.0e'))
+
+        #sets the figure to a tight layout
+        fig.tight_layout()
+
+        #shows the figure where you can zoom/resize at will, and save to a file (recommended to save as a .svg for figure scaling)
+        plt.show()
+
+    def plottic(self):
+        file = self.ui.fileLineedit.text()
+        exp1 = oms.MSExperiment()
+        oms.MzMLFile().load(file, exp1)
+        fig, axs = plt.subplots()
+        fig.set_figheight(4)
+        plt.subplots_adjust(hspace=1)
+        for chrom in exp1.getChromatograms():
+            retention_times, intensities = chrom.get_peaks()
+            axs.plot(retention_times, intensities, self.ui.colourBox.currentText(), linewidth = self.ui.widthBox.value())
+        axs.set_xlabel("time (s)")
+        axs.set_ylabel("Counts")
+        #set the y-axis upper and lower limits - accepts raw integers or scientific notation
+        axs.set_ylim(self.ui.lowySpinbox.value(), self.ui.highySpinbox.value())
+
+        #Set the x-axis upper and lower limit - accepts raw integers or scientific notation
+        axs.set_xlim(self.ui.lowscanSpinbox.value(), self.ui.highscanSpinbox.value())
+        axs.yaxis.set_major_formatter(ticker.FormatStrFormatter('%0.0e'))
+        plt.tight_layout()
+        plt.show()
+
+    def ploteic(self):
+        file = self.ui.fileLineedit.text()
+
+        # load MS data and store as MSExperiment object
+        exp1 = oms.MSExperiment()
+        oms.MzMLFile().load(file, exp1)
+
+        mz_values = [self.ui.mzSpinbox.value()]
+        print(len(exp1.getSpectra()))
+        intensity_values = []
+        for i in range(0, len(exp1.getSpectra())):
+            current_spectrum = exp1.getSpectra()[i]
+            for mz_value in mz_values:
+                intensity = self.extract_intensity(current_spectrum, mz_value)
+                if intensity is not None: # if intensity is none, the value will not be added to the list and the corresponding scan in the final output will read 0
+                    intensity_values.append(intensity)
+        fig, axs = plt.subplots()
+        fig.set_figheight(4)
+        plt.subplots_adjust(hspace=1)
+        axs.plot(intensity_values, self.ui.colourBox.currentText(), linewidth = self.ui.widthBox.value())
+
+        axs.set_xlabel("Scan")
+        axs.set_ylabel("Counts")
+        #set the y-axis upper and lower limits - accepts raw integers or scientific notation
+        axs.set_ylim(self.ui.lowySpinbox.value(), self.ui.highySpinbox.value())
+
+        #Set the x-axis upper and lower limit - accepts raw integers or scientific notation
+        axs.set_xlim(self.ui.lowscanSpinbox.value(), self.ui.highscanSpinbox.value())
+        axs.yaxis.set_major_formatter(ticker.FormatStrFormatter('%0.0e'))
+        plt.tight_layout()
+        plt.legend()
+        plt.show()
+
+
+if __name__ == '__main__':
+    app = QApplication(sys.argv)
+    GUI = MainWindow()
+    sys.exit(app.exec())