#!/usr/bin/env python3
# 2025 (c) Micha Johannes Birklbauer
# https://github.com/michabirklbauer/
# micha.birklbauer@gmail.com
from __future__ import annotations
import pandas as pd
from matplotlib import pyplot as plt
from matplotlib.figure import Figure
from ..data._csm import CrosslinkSpectrumMatch
from ..data._util import check_input
from ..transform._filter import filter_peptide_pair_distribution
from typing import Optional
from typing import List
from typing import Tuple
from typing import Any
[docs]
def plot_peptide_pair_distribution(
data: List[CrosslinkSpectrumMatch],
top_n: int = 25,
color: str = "#6d4bff",
title: str = "Peptide Pair Distribution",
figsize: Tuple[float, float] = (16.0, 9.0),
filename_prefix: Optional[str] = None,
) -> Tuple[Figure, Any]:
r"""Plot the peptide pair distribution for a set of crosslink-spectrum-matches.
Plot the peptide pair distribution as a barplot for a set of crosslink-spectrum-matches.
Parameters
----------
data : list of CrosslinkSpectrumMatch
A list of crosslink-spectrum-matches.
top_n : int, default = 25
Number of peptide pairs to plot. Peptide pairs are sorted by number of
crosslink-spectrum-matches.
color : str, default = "#6d4bff"
Color of the bars.
title : str, default = "Peptide Pair Distribution"
The title of the barplot.
figsize : tuple of float, float, default = (16.0, 9.0)
Width, height in inches.
filename_prefix : str, or None
If given, plot will be saved with and without title in .png and .svg format with the given
prefix.
Returns
-------
tuple of matplotlib.figure.Figure, any
The created figure and axis ``from matplotlib.pyplot.subplots()``.
Raises
------
TypeError
If a wrong data type is provided.
ValueError
If parameter data does not contain any crosslink-spectrum-matches.
Examples
--------
>>> from pyXLMS import parser
>>> from pyXLMS import plotting
>>> pr = parser.read_msannika(
... "data/ms_annika/XLpeplib_Beveridge_QEx-HFX_DSS_R1_CSMs.xlsx"
... )
>>> csms = pr["crosslink-spectrum-matches"]
>>> fig, ax = plotting.plot_peptide_pair_distribution(csms)
"""
_ok = check_input(data, "data", list, CrosslinkSpectrumMatch)
_ok = check_input(top_n, "top_n", int)
_ok = check_input(color, "color", str)
_ok = check_input(title, "title", str)
_ok = check_input(figsize, "figsize", tuple)
_ok = (
check_input(filename_prefix, "filename_prefix", str)
if filename_prefix is not None
else True
)
if len(data) == 0:
raise ValueError(
"Can't plot peptide pair distribution if no crosslink-spectrum-matches are given!"
)
pps = filter_peptide_pair_distribution(data)
pp_names = list()
pp_total = list()
for pp in pps:
pp_names.append(pp)
pp_total.append(len(pps[pp]))
sorted = pd.DataFrame(
{
"peptide_pair": pp_names,
"total": pp_total,
}
).sort_values(by="total", axis=0, ascending=False)
pp_names = sorted["peptide_pair"].values.tolist()[:top_n]
pp_total = sorted["total"].values.tolist()[:top_n]
fig, ax = plt.subplots(figsize=figsize)
bar = ax.bar(pp_names, pp_total, color=color)
ax.bar_label(bar, padding=3.0)
ax.set_xticks(range(len(pp_names)), pp_names, rotation=45, ha="right")
ax.set_ylabel("Number of crosslink-spectrum-matches")
ax.set_xlabel("Peptide Pair")
if filename_prefix is not None:
plt.savefig(
filename_prefix + "_notitle.png",
dpi=300,
transparent=True,
bbox_inches="tight",
)
plt.savefig(
filename_prefix + "_notitle.svg",
dpi=300,
transparent=True,
bbox_inches="tight",
)
ax.set_title(title)
plt.savefig(
filename_prefix + ".png", dpi=300, transparent=True, bbox_inches="tight"
)
plt.savefig(
filename_prefix + ".svg", dpi=300, transparent=True, bbox_inches="tight"
)
else:
ax.set_title(title)
return (fig, ax)
