Environment Setup and Configuration

installation¶

1. Python¶

git  clone https://github.com/Anglejuebi/HiSTaR
cd HiSTaR
python setup.py build
python setup.py install

2.Anaconda (recommend)¶

conda create -n HiSTaR python=3.11

conda activate HiSTaR

git clone https://github.com/Anglejuebi/HiSTaR

cd HiSTaR

python setup.py build

python setup.py install

Use HiSTaR in notebook¶

pip install ipykernel

python -m ipykernel install --user --name=HiSTaR

HiSTaR needs to use R mclust for clustering. If you encounter errors, you can manually download R and install mclust, and then modify your path in the HiSTaR.configure_r_environment¶

HiSTaR.configure_r_environment
{
    try:
        ctypes.CDLL(r"D:\R-4.4.2\bin\x64\Rblas.dll") #replace your path
        ctypes.CDLL(r"D:\R-4.4.2\bin\x64\Rlapack.dll") #replace your path
        # print("Rblas.dll and Rlapack.dll load successful！")
    except Exception as e:
        print(f"load error：{e}")

    import os
    from pathlib import Path
    import ctypes
    r_bin = Path("D:/R-4.4.2/bin/x64") #replace your path
    ctypes.CDLL(str(r_bin / "Rblas.dll")) #replace your path
    ctypes.CDLL(str(r_bin / "Rlapack.dll")) #replace your path

    os.environ['R_HOME'] = str(r_bin.parent.parent)
    os.environ['PATH'] = f"{r_bin};{os.environ.get('PATH', '')}"

    import rpy2.robjects as robjects
    from rpy2.rinterface_lib import openrlib
    openrlib.rlib.R_set_command_line_arguments(0, [])

    test_code = '''
        x <- matrix(c(1,2,3,4), 2, 2)
        # print("Testing simple SVD:")
        try({
            result <- La.svd(x)
            # print(result)
        }, silent=FALSE)
    '''
    result = robjects.r(test_code)
    # print(result)

    os.environ['R_HOME'] = 'D:/R-4.4.2' #replace your path
    os.environ['R_USER'] = os.path.expanduser('~') #replace your path
    os.environ['PATH'] = 'D:/R-4.4.2/bin/x64;' + os.environ['PATH'] #replace your path
    os.environ['R_LIBS'] = 'D:/R-4.4.2/library' #replace your path
}