#!/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._crosslink import Crosslink
from ..data._util import check_input
from ..transform._util import check_available_keys
from ..transform._util import assert_csms_or_xls
from ..transform._filter import filter_protein_distribution
from ..transform._filter import filter_crosslink_type
from typing import Optional
from typing import List
from typing import Tuple
from typing import Any
[docs]
def plot_protein_distribution(
data: List[CrosslinkSpectrumMatch] | List[Crosslink],
top_n: int = 25,
colors: List[str] = ["#6d4bff", "#ac99ff"],
title: str = "Protein Distribution",
figsize: Tuple[float, float] = (16.0, 9.0),
filename_prefix: Optional[str] = None,
) -> Tuple[Figure, Any]:
r"""Plot the protein distribution for a set of crosslink-spectrum-matches or crosslinks.
Plot the protein distribution as a barplot for a set of crosslink-spectrum-matches or crosslinks.
Parameters
----------
data : list of CrosslinkSpectrumMatch, or list of Crosslink
A list of crosslink-spectrum-matches or crosslinks.
top_n : int, default = 25
Number of proteins to plot. Proteins are sorted by number of crosslinks
or crosslink-spectrum-matches.
colors : list of str, default = ["#6d4bff", "#ac99ff"]
Colors of the bar-types (intra-link and inter-link).
title : str, default = "Protein 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 or crosslinks.
ValueError
If attribute 'alpha_proteins', or 'beta_proteins' is not available for any of the data.
IndexError
If not enough colors where specified.
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_protein_distribution(csms)
"""
_ok = check_input(data, "data", list)
_ok = check_input(top_n, "top_n", int)
_ok = check_input(colors, "colors", list, 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(colors) < 2:
raise IndexError("At least two colors need to be given for the plot!")
if len(data) == 0:
raise ValueError(
"Can't plot protein distribution if no crosslink-spectrum-matches or crosslinks are given!"
)
data = assert_csms_or_xls(data)
_ok = check_available_keys(["alpha_proteins", "beta_proteins"], data)
ylabel = (
"crosslink-spectrum-matches"
if data[0]["data_type"] == "crosslink-spectrum-match"
else "crosslinks"
)
proteins = filter_protein_distribution(data)
protein_names = list()
protein_intra = list()
protein_inter = list()
protein_total = list()
for protein in proteins:
protein_names.append(protein)
intra_inter = filter_crosslink_type(proteins[protein])
protein_intra.append(len(intra_inter["Intra"]))
protein_inter.append(len(intra_inter["Inter"]))
protein_total.append(len(proteins[protein]))
sorted = pd.DataFrame(
{
"protein": protein_names,
"intra": protein_intra,
"inter": protein_inter,
"total": protein_total,
}
).sort_values(by="total", axis=0, ascending=False)
protein_names = sorted["protein"].values.tolist()[:top_n]
protein_intra = sorted["intra"].values.tolist()[:top_n]
protein_inter = sorted["inter"].values.tolist()[:top_n]
fig, ax = plt.subplots(figsize=figsize)
bottom = [0.0 for i in protein_names]
bar = ax.bar(
protein_names, protein_intra, label="intra-link", bottom=bottom, color=colors[0]
)
bottom = protein_intra
ax.bar_label(bar, label_type="center")
bar = ax.bar(
protein_names, protein_inter, label="inter-link", bottom=bottom, color=colors[1]
)
bottom = protein_inter
ax.bar_label(bar, label_type="center")
ax.set_xticks(range(len(protein_names)), protein_names, rotation=45, ha="right")
ax.legend(loc="upper right")
ax.set_ylabel(f"Number of {ylabel}")
ax.set_xlabel("Protein")
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)
