Merge pull request #50 from xomicsdatascience/spectra_plotting

added plotting functions for spectra and spectra comparison

csodiaq/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '1.1.6'
+__version__ = '1.1.7'
 
 from csodiaq import csodiaq_gui, csodiaq, csodiaq_identification_functions, csodiaq_mgf_cleaning_functions, \
     csodiaq_quantification_functions, idpicker, IdentificationSpectraMatcher, spectra_matcher_functions

csodiaq/plotting/__init__.py

@@ -0,0 +1 @@
+from . import spectra

csodiaq/plotting/spectra.py

@@ -0,0 +1,60 @@
+import pyteomics.mzxml
+from matplotlib import pyplot as plt
+from csodiaq.spectrum import Spectrum
+
+
+def spectrum_lineplot(spectrum: Spectrum,
+                      positive: bool = True,
+                      color: str = 'black',
+                      label: str = None):
+    """
+    Plots the input Spectrum as a line plot
+    Parameters
+    ----------
+    spectrum : Spectrum
+        Spectrum object
+    positive : bool
+        Whether plot should have positive or negative intensities
+    color : str
+        Color for the line in the plot.
+    label : str
+        Label to use for the legend.
+
+    Returns
+    -------
+    None
+    """
+    intensity = spectrum.intensity
+    max_intensity = max(intensity)
+    intensity = [i/max_intensity for i in intensity]
+    if not positive:
+        intensity = [-i for i in intensity]
+    plt.vlines(spectrum.mz, [0]*len(intensity), intensity, colors=color, label=label)
+    plt.hlines(0, min(spectrum.mz), max(spectrum.mz), colors='black')
+    return
+
+
+def spectrum_comparison_lineplot(spectrum_positive: Spectrum,
+                                 spectrum_negative: Spectrum,
+                                 colors: list = ('dodgerblue', 'purple'),
+                                 labels: list = None):
+    """
+    Produces a plot with input Spectrum in positive/negative y directions.
+    Parameters
+    ----------
+    spectrum_positive : Spectrum
+        Spectrum to plot with positive intensity.
+    spectrum_negative : Spectrum
+        Spectrum to plot with negative intensity.
+    colors : list
+        List of colors to use for the plots.
+    labels : list
+        List of labels to use for the legends.
+    Returns
+    -------
+    None
+    """
+    plt.figure()
+    spectrum_lineplot(spectrum_positive, positive=True, color=colors[0], label=labels[0])
+    spectrum_lineplot(spectrum_negative, positive=False, color=colors[1], label=labels[1])
+    return