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Figure_1_Figure_Supplement_3.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jul 5 16:13:51 2022
@author: scottrk
"""
import os
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.patches as Patch
from matplotlib.lines import Line2D
import seaborn as sns
from GlobalVars_ import young_mouse_id, old_mouse_id, tissue_type, \
tissue_type_long, color_cycle
from compile_data import summary_import
def collate_copy_num_data(copy_num_table, summary_data):
freq_SNV_data = []
freq_InDel_data = []
copy_num_data = []
tissue_list = []
for group in [young_mouse_id, old_mouse_id]:
for mouse in group:
mouseid = mouse.split('_')[0]
for tissue in tissue_type[:-1]:
if mouseid in list(copy_num_table['Mouse_ID']):
try:
copy_num_val = copy_num_table.query("Mouse_ID==@mouseid & Tissue_Abbrev==@tissue")[
'mt_tert_ratio']
if str(list(copy_num_val)[0]) != 'nan':
freq_SNV_data.append(
float(summary_data.query("MouseID==@mouseid & Tissue==@tissue")['Total_SNV_Freq']))
freq_InDel_data.append(
float(summary_data.query("MouseID==@mouseid & Tissue==@tissue")['Total_InDel_Freq']))
copy_num_data.append(float(copy_num_val))
tissue_list.append(tissue)
except:
pass
df = pd.DataFrame([freq_SNV_data,
freq_InDel_data,
copy_num_data,
tissue_list],
index=["SNV_Freq", "InDel_Freq", "Copy_Num", "Tissue"]
).T
df.query("Tissue!='Blood'", inplace=True)
return df
def setup_figure():
fig, axs = plt.subplots(nrows=3, layout='constrained', figsize=(6, 12))
axs[1].margins(x=0, y=0)
axs[2].margins(x=0, y=0)
return fig, axs
def plot_subplot_A(ax):
sns.boxplot(x="Tissue_Abbrev", y="mt_tert_ratio", hue="Group",
hue_order=['Young', 'Aged', 'ELAM'], data=copy_num_data,
order=tissue_type[:-1], flierprops=dict(marker='o', color='black'),
whiskerprops=dict(color='black'), medianprops=dict(color='black'),
linewidth=1.5, ax=ax)
ax.set_ylim(0, 15000)
ax.set_xlabel("Tissue", fontsize=16)
ax.set_ylabel("mtDNA:nDNA", fontsize=14)
ax.set_xticklabels(tissue_type_long, fontdict={'rotation': 45}, fontsize=14)
legend = [Patch.Patch(facecolor='white', edgecolor='black', label='Young'),
Patch.Patch(facecolor='lightgrey', edgecolor='black', label='Old'),
Patch.Patch(facecolor='lightgrey', edgecolor='black', label='Elam', hatch='///')]
ax.legend(handles=legend, title='Group')
fc = ['#FFFFFF', '#FFFFFF', '#FFFFFF', '#ff9200', '#FFFFFF', '#ff9200',
'#FFFFFF', '#0433ff', '#0433ff', '#FFFFFF', '#ff84ff', '#ff84ff',
'#FFFFFF', '#76d5ff', '#76d5ff', '#FFFFFF', '#932191', '#932191',
'#FFFFFF', '#935200', '#935200', '#FFFFFF', '#008e00', '#008e00',
'#FFFFFF', '#ff2600', '#ff2600'
]
ec = ['black', '#ff9200', 'black', 'black', 'black', 'black', '#0433ff',
'black', 'black', '#ff84ff', 'black', 'black', '#76d5ff', 'black',
'black', '#932191', 'black', 'black', '#935200', 'black', 'black',
'#008e00', 'black', 'black', '#ff2600', 'black', 'black'
]
for i, bar in enumerate(ax.patches):
ax.patches[i].set_facecolor(fc[i])
ax.patches[i].set_edgecolor(ec[i])
if i in [5, 8, 11, 14, 17, 20, 23, 26]:
bar.set_hatch('///')
def plot_subplot_B_C(ax, y, ylabel, xlabel="mtDNA:nDNA"):
sns.scatterplot(x='Copy_Num', y=y, hue='Tissue', data=collated_data,
hue_order=tissue_type[:-1], palette=color_cycle, ax=ax)
ax.legend(handles=[Line2D([0], [0], marker='o', color='w',
markerfacecolor=color_cycle[i],
markersize=10) for i in range(0, 8)],
labels=tissue_type_long,
title="Tissue",
ncol=2)
plt.setp(ax.get_yaxis().get_offset_text(), visible=False)
ax.set_ylabel(ylabel, fontsize=14)
ax.set_xlabel(xlabel, fontsize=14)
if __name__ == "__main__":
copy_num_data = pd.read_csv("data/misc_items/mito_copy_number_data.csv")
collated_data = collate_copy_num_data(copy_num_data,
summary_import("data/Mouse_aging_mtDNA_summary.csv")
)
fig, axs = setup_figure()
plot_subplot_A(axs[0])
plot_subplot_B_C(axs[1], y="SNV_Freq",
ylabel="SNV Frequency ($\mathregular{10^{-6}}$)")
plot_subplot_B_C(axs[2], y="SNV_Freq",
ylabel="In/Del Frequency ($\mathregular{10^{-6}}$)")
if not os.path.isdir("figures"):
os.mkdir("figures/")
fig.savefig('figures/Figure_1_Figure_Supplement_3.png', dpi=600, facecolor='white')
fig.savefig('figures/Figure_1_Figure_Supplement_3.pdf', dpi=600, facecolor='white')