.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "gallery/ms_bokeh/plot_spyogenes_subplots_ms_bokeh.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. or to run this example in your browser via Binder .. rst-class:: sphx-glr-example-title .. _sphx_glr_gallery_ms_bokeh_plot_spyogenes_subplots_ms_bokeh.py: Plot Spyogenes subplots ms_bokeh ======================================= Here we show how we can plot multiple chromatograms across runs together .. GENERATED FROM PYTHON SOURCE LINES 7-99 .. bokeh-plot:: :source-position: none from bokeh.plotting import show import pandas as pd import requests import zipfile import numpy as np from bokeh.layouts import column from bokeh.io import show import pandas as pd import requests import numpy as np from bokeh.layouts import column from bokeh.io import show ###### Load Data ####### # URL of the zip file url = "https://github.com/OpenMS/pyopenms_viz/releases/download/v0.1.3/spyogenes.zip" zip_filename = "spyogenes.zip" # Download the zip file try: print(f"Downloading {zip_filename}...") response = requests.get(url) response.raise_for_status() # Check for any HTTP errors # Save the zip file to the current directory with open(zip_filename, "wb") as out: out.write(response.content) print(f"Downloaded {zip_filename} successfully.") except requests.RequestException as e: print(f"Error downloading zip file: {e}") except IOError as e: print(f"Error writing zip file: {e}") # Unzipping the file try: with zipfile.ZipFile(zip_filename, "r") as zip_ref: # Extract all files to the current directory zip_ref.extractall() print("Unzipped files successfully.") except zipfile.BadZipFile as e: print(f"Error unzipping file: {e}") annotation_bounds = pd.read_csv( "spyogenes/AADGQTVSGGSILYR3_manual_annotations.tsv", sep="\t" ) # contain annotations across all runs chrom_df = pd.read_csv( "spyogenes/chroms_AADGQTVSGGSILYR3.tsv", sep="\t" ) # contains chromatogram for precursor across all runs ##### Set Plotting Variables ##### pd.options.plotting.backend = "ms_bokeh" RUN_NAMES = [ "Run #0 Spyogenes 0% human plasma", "Run #1 Spyogenes 0% human plasma", "Run #2 Spyogenes 0% human plasma", "Run #3 Spyogenes 10% human plasma", "Run #4 Spyogenes 10% human plasma", "Run #5 Spyogenes 10% human plasma", ] # For each run fill in the axs object with the corresponding chromatogram plot_list = [] for i, run in enumerate(RUN_NAMES): run_df = chrom_df[chrom_df["run_name"] == run] current_bounds = annotation_bounds[annotation_bounds["run"] == run] plot_list.append( run_df.plot( kind="chromatogram", x="rt", y="int", grid=False, by="ion_annotation", title=run_df.iloc[0]["run_name"], title_font_size=16, width=700, xaxis_label_font_size=16, yaxis_label_font_size=16, xaxis_tick_font_size=14, yaxis_tick_font_size=14, relative_intensity=True, annotation_data=current_bounds, xlabel="Retention Time (sec)", ylabel="Relative\nIntensity", show_plot=False, legend_config={"show": True, "title": "Transition"}, ) ) show(column(plot_list)) .. rst-class:: sphx-glr-script-out .. code-block:: none Downloading spyogenes.zip... Downloaded spyogenes.zip successfully. Unzipped files successfully. | .. code-block:: Python import pandas as pd import requests import zipfile import numpy as np from bokeh.layouts import column from bokeh.io import show import pandas as pd import requests import numpy as np from bokeh.layouts import column from bokeh.io import show ###### Load Data ####### # URL of the zip file url = "https://github.com/OpenMS/pyopenms_viz/releases/download/v0.1.3/spyogenes.zip" zip_filename = "spyogenes.zip" # Download the zip file try: print(f"Downloading {zip_filename}...") response = requests.get(url) response.raise_for_status() # Check for any HTTP errors # Save the zip file to the current directory with open(zip_filename, "wb") as out: out.write(response.content) print(f"Downloaded {zip_filename} successfully.") except requests.RequestException as e: print(f"Error downloading zip file: {e}") except IOError as e: print(f"Error writing zip file: {e}") # Unzipping the file try: with zipfile.ZipFile(zip_filename, "r") as zip_ref: # Extract all files to the current directory zip_ref.extractall() print("Unzipped files successfully.") except zipfile.BadZipFile as e: print(f"Error unzipping file: {e}") annotation_bounds = pd.read_csv( "spyogenes/AADGQTVSGGSILYR3_manual_annotations.tsv", sep="\t" ) # contain annotations across all runs chrom_df = pd.read_csv( "spyogenes/chroms_AADGQTVSGGSILYR3.tsv", sep="\t" ) # contains chromatogram for precursor across all runs ##### Set Plotting Variables ##### pd.options.plotting.backend = "ms_bokeh" RUN_NAMES = [ "Run #0 Spyogenes 0% human plasma", "Run #1 Spyogenes 0% human plasma", "Run #2 Spyogenes 0% human plasma", "Run #3 Spyogenes 10% human plasma", "Run #4 Spyogenes 10% human plasma", "Run #5 Spyogenes 10% human plasma", ] # For each run fill in the axs object with the corresponding chromatogram plot_list = [] for i, run in enumerate(RUN_NAMES): run_df = chrom_df[chrom_df["run_name"] == run] current_bounds = annotation_bounds[annotation_bounds["run"] == run] plot_list.append( run_df.plot( kind="chromatogram", x="rt", y="int", grid=False, by="ion_annotation", title=run_df.iloc[0]["run_name"], title_font_size=16, width=700, xaxis_label_font_size=16, yaxis_label_font_size=16, xaxis_tick_font_size=14, yaxis_tick_font_size=14, relative_intensity=True, annotation_data=current_bounds, xlabel="Retention Time (sec)", ylabel="Relative\nIntensity", show_plot=False, legend_config={"show": True, "title": "Transition"}, ) ) show(column(plot_list)) .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 1.043 seconds) .. _sphx_glr_download_gallery_ms_bokeh_plot_spyogenes_subplots_ms_bokeh.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://notebooks.gesis.org/binder/v2/gh/OpenMS/pyopenms_viz/gh_pages?filepath=notebooks/gallery/ms_bokeh/plot_spyogenes_subplots_ms_bokeh.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_spyogenes_subplots_ms_bokeh.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_spyogenes_subplots_ms_bokeh.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_spyogenes_subplots_ms_bokeh.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_