Plotting Target and Decoy Distribution


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

✓


    Installed pyXLMS version: 1.3.0


from pyXLMS import parser
from pyXLMS import plotting

All plotting functionality is available via the plotting submodule. We also import the parser submodule here for reading result files.


parser_result = parser.read(
    "../../data/ms_annika/XLpeplib_Beveridge_QEx-HFX_DSS_R1.pdResult",
    engine="MS Annika",
    crosslinker="DSS",
)

✓


    Reading MS Annika CSMs...: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████| 826/826 [00:00<00:00, 12467.15it/s]
    Reading MS Annika crosslinks...: 100%|██████████████████████████████████████████████████████████████████████████████████████████████| 300/300 [00:00<00:00, 18755.55it/s]

We read crosslink-spectrum-matches and crosslinks using the generic parser from a single .pdResult file.


fig, ax = plotting.plot_target_decoy_distribution(
    parser_result["crosslink-spectrum-matches"],
    figsize=(7.0, 4.0),
    filename_prefix="target_decoy_dist_csms",
)

png

We can plot the target-decoy distribution for our crosslink-spectrum-matches by passing them as the first argument.

Important

Please note that plotting a target-decoy distribution is only possible if all data have associated target-decoy labels, otherwise the function will raise an exception!

The default figure size is 16 by 9 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_target_decoy_distribution(
    parser_result["crosslinks"],
    title="Target-Target and Decoy-Decoy Distribution",
    figsize=(7.0, 4.0),
)

png

We can do the same plot for our crosslinks by passing them as the first argument instead. As a side note, you can see here that MS Annika only uses Decoy-Decoy labels for all decoy crosslinks, not matter if they are Decoy-Decoy or Target-Decoy matches. This time we also 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 colors, you can read more about all the possible parameters here: docs.