fEEMS.md

Playing with fEEMS

Copied from https://github.com/NovembreLab/feems with modifications.

Set up in bash terminal:

conda create -n=feems_e python=3.8.3 

conda activate feems_e

conda install -c conda-forge suitesparse=5.7.2 scikit-sparse=0.4.4 cartopy=0.18.0 jupyter=1.0.0 jupyterlab=2.1.5 sphinx=3.1.2 sphinx_rtd_theme=0.5.0 nbsphinx=0.7.1 sphinx-autodoc-typehints

pip install git+https://github.com/NovembreLab/feems

activate python environment:

python

Follow tutorial: https://github.com/NovembreLab/feems/blob/main/docsrc/notebooks/getting-started.ipynb

base

import numpy as np

import pkg_resources

from sklearn.impute import SimpleImputer

from pandas_plink import read_plink

viz

import matplotlib.pyplot as plt

import cartopy.crs as ccrs

feems

from feems.utils import prepare_graph_inputs

from feems import SpatialGraph, Viz

change matplotlib fonts

plt.rcParams["font.family"] = "Arial"

plt.rcParams["font.sans-serif"] = "Arial"

data_path = pkg_resources.resource_filename("feems", "data/")