oktoberfest.pl.plot_sa_distribution

oktoberfest.pl.plot_sa_distribution(prosit_df, target_df, decoy_df, filename)

Generate spectral angle distribution for targets and decoys.

Parameters:

  • prosit_df (DataFrame) – mokapot / percolator input tab for rescoring with peptide property prediction

  • target_df (DataFrame) – mokapot / percolator target output for rescoring with peptide property prediction on the psm level

  • decoy_df (DataFrame) – mokapot / percolator decoy output for rescoring with peptide property prediction on the psm level

  • filename (Path) – the path to the location used for storing the plot

Example:

>>> from oktoberfest import plotting as pl
>>> import pandas as pd
>>> # Required columns: SpecId and spectral_angle
>>> prosit_df = pd.DataFrame({"SpecId": ["F1-15-TAIASPEK-1-5","F2-59-LGLTKLQLH-3-9","F1-24-EFAVEVLK-2-4",
>>>                         "F2-63-ISDPTSPLRTR-2-9","F1-16-ADHPLRTR-1-5","F1-11-KLYNANYIK-3-7","F2-4-YLNPLRTK-1-5"],
>>>                         "spectral_angle": [0.6,0.2,0.3,0.6,0.4,0.2,0.5]})
>>> # Required columns: PSMId, score, q-value and peptide
>>> target_df = pd.DataFrame({"PSMId": ["F1-15-TAIASPEK-1-5","F2-59-LGLTKLQLH-3-9","F1-24-EFAVEVLK-2-4",
>>>                         "F2-63-ISDPTSPLRTR-2-9","F1-16-ADHPLRTR-1-5","F2-4-YLNPLRTK-1-5"],
>>>                         "q-value": [0.005,0.008,0.002,0.006,0.004,0.001],
>>>                         "score": [-0.1,-0.5,-0.5,0.7,0.4,0.5],
>>>                         "peptide": ["TAIASPEK","LGLTKLQLH","EFAVEVLK","ISDPTSPLRTSR","ADHPLRTR","YLNPLRTK"]})
>>> decoy_df = pd.DataFrame({"PSMId": ["F1-11-KLYNANYIK-3-7","F2-59-LGLTKLQLH-3-9","F1-24-EFAVEVLK-2-4"],
>>>                         "q-value": [0.006,0.004,0.003],
>>>                         "score": [-0.1,-0.5,-0.5],
>>>                         "peptide": ["KLYNANYIK","LGLTKLQLH","EFAVEVLK"]})
>>> pl.plot_sa_distribution(prosit_df=prosit_df,
>>>                         target_df=target_df,
>>>                         decoy_df=decoy_df,
>>>                         filename="./tests/doctests/output/sa_distribution_plot.svg")