Plotting Venn Diagrams

from pyXLMS import __version__
 
print(f"Installed pyXLMS version: {__version__}")

    Installed pyXLMS version: 1.1.2

from pyXLMS import pipelines
from pyXLMS import plotting

All plotting functionality is available via the plotting submodule. We also import the pipelines submodule here for reading crosslink-spectrum-match result files and doing some standard data transformations.

%%capture output
 
msannika = pipelines.pipeline(
    "../../data/ms_annika/XLpeplib_Beveridge_QEx-HFX_DSS_R1_CSMs.txt",
    engine="MS Annika",
    crosslinker="DSS",
)
csms_msannika = msannika["crosslink-spectrum-matches"]
 
maxquant = pipelines.pipeline(
    "../../data/maxquant/run1/crosslinkMsms.txt", engine="MaxQuant", crosslinker="DSS"
)
csms_maxquant = maxquant["crosslink-spectrum-matches"]
 
plink = pipelines.pipeline(
    "../../data/plink2/Cas9_plus10_2024.06.20.filtered_cross-linked_spectra.csv",
    engine="pLink",
    crosslinker="DSS",
)
csms_plink = plink["crosslink-spectrum-matches"]

We read crosslink-spectrum-matches from three different search engines (MS Annika, MaxQuant, pLink) that searched the same RAW file using pipelines.pipepline(). Additionally, the pipeline will automatically filter for unique crosslink-spectrum-matches, validate them for estimated 1% FDR and only keep target-target hits. You can read more about the pipeline here: docs.

We use the %%capture magic here to not display the information that is printed by pipelines.pipeline() in order to not clutter the notebook, feel free to disable this in your own run to see exactly what pipelines.pipeline() does!

fig, ax = plotting.plot_venn_diagram(
    csms_msannika,
    csms_maxquant,
    labels=["MS Annika", "MaxQuant"],
    colors=["#4361EE", "#4CC9F0"],
    figsize=(5.0, 5.0),
    filename_prefix="MS Annika & MaxQuant",
)

We can plot the 2-set venn diagram for MS Annika and MaxQuant crosslink-spectrum-matches by passing them as the first two arguments. You can control the labels and colors via the labels and colors parameters. The default figure size is 10 by 10 inches and does not need to be set explicitly, we just used a smaller one here for demonstration purposes. The filename_prefix parameter is also optional, if it is given the plot is saved four times: once without the title in .png and .svg format, and once with the title in .png and .svg format.

fig, ax = plotting.plot_venn_diagram(
    csms_msannika,
    csms_maxquant,
    csms_plink,
    labels=["MS Annika", "MaxQuant", "pLink"],
    contour=True,
    title="Venn diagram for CMSs of XLpeplib_Beveridge_QEx-HFX_DSS_R1",
    figsize=(5.0, 5.0),
)

We can plot the 3-set venn diagram for MS Annika, MaxQuant and pLink crosslink-spectrum-matches by passing them as the first three arguments. This time we also specify contour=True to draw a contour around the circles and additionally specify a title for our plot via the title parameter. Since we did not specify a filename_prefix the plot is not saved to disk. There are also other parameters that can be set to tune your plot like alpha and linewidth, you can read more about all the possible parameters here: docs.