.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "gallery/ms_plotly/plot_spyogenes_subplots_ms_plotly.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_plotly_plot_spyogenes_subplots_ms_plotly.py: Plot Spyogenes subplots ms_plotly ======================================= Here we show how we can plot multiple chromatograms across runs together. In this rendering the plot is slightly cut off .. GENERATED FROM PYTHON SOURCE LINES 7-96 .. rst-class:: sphx-glr-script-out .. code-block:: none Downloading spyogenes.zip... Downloaded spyogenes.zip successfully. Unzipped files successfully. .. raw:: html

| .. code-block:: Python import pandas as pd import requests import zipfile import numpy as np from plotly.subplots import make_subplots ###### Load/Download 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_plotly" 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", 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"}, ) ) # Combine all plots into plotly subplot fig = make_subplots(rows=len(plot_list), cols=1, subplot_titles=RUN_NAMES) for idx, f in enumerate(plot_list): for trace in f.data: fig.add_trace(trace, row=idx + 1, col=1) fig .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 0.599 seconds) .. _sphx_glr_download_gallery_ms_plotly_plot_spyogenes_subplots_ms_plotly.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_plotly/plot_spyogenes_subplots_ms_plotly.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_spyogenes_subplots_ms_plotly.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_spyogenes_subplots_ms_plotly.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_spyogenes_subplots_ms_plotly.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_