Added plot utilities and label mapping code

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'''

This file contains standardized imports and variables used throughout the 

analysis notebooks for "Progressive Plasticity in Colorectal Cancer Metastasis"

by Moorman et al (DOI: )

'''

# Packages used throughout

import scanpy as sc

import anndata

import numpy as np

import scipy as sp

import pandas as pd

from matplotlib import pyplot as plt

import os

import sys

import json

import tqdm

# Local modules used throughout

module_path = os.path.abspath('../src')

if module_path not in sys.path:

    sys.path.append(module_path)

# Standard variables referenced throughout

data_dir = f"{os.getcwd()}/../data"

media_dir = f"{os.getcwd()}/../media"

# Plotting styles used throughout

module_path = os.path.abspath('../src')

stylesheet = f'{module_path}/utils/pl/assets/default.mplstyle'

plt.style.use(stylesheet)

with open(f'{module_path}/utils/pl/assets/named_colors.json', 'r') as f:

    named_colors = json.load(f)

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[build-system]

requires = ["setuptools>=58.0.0", "wheel"]

build-backend = "setuptools.build_meta"

[project]

name = "my_project"

version = "1.0.0"

description = "My project description"

authors = ["Andrew Moorman <moormana@mskcc.org>"]

license = "MIT"

keywords = []

classifiers = []

requires-python = ">=3.8"

dependencies = [

    "scanpy",

    "matplotlib",

    "pandas",

    "numpy",

    "seaborn",

    "openpyxl",

    "scipy",

    "scikit-misc",

    "PhenoGraph",

    "magic-impute",

    "python-ternary",

]

figure.dpi : 300

font.family : "Arial"

mathtext.default : "default"

xtick.labelsize : 7

ytick.labelsize : 7

axes.labelsize : 9

axes.titlesize : 9

axes.facecolor : "white"

xtick.direction : "out"

ytick.direction : "out"

image.cmap : "viridis"

lines.linewidth : 0.75

axes.spines.right : False

axes.spines.top : False

legend.borderaxespad : 0.25

legend.borderpad : 0.25

legend.fontsize : 7

legend.title_fontsize : 7

legend.handleheight : 0.5

legend.handlelength : 1.0

legend.markerscale : 0.5

patch.linewidth : 0.75

axes.prop_cycle : cycler("color", ["#F04437", "#E81F64", "#903E97", "#65499E", "#4356A5", "#478FCC", "#34A4DD", "#00BCD4", "#009889", "#4BB04F", "#8BC34C", "#CCDA3A", "#FCED3A", "#FFC10E", "#F8991D", "#F1592C", "#7A5649", "#9F9E9E", "#607F8C",])

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