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CostaLab / CrossTalkeR

R package to do the Ligand Receptor Analysis Visualization
https://costalab.github.io/CrossTalkeR/
MIT License
41 stars 10 forks source link

parserR2py #58

Open jsnagai opened 3 weeks ago

jsnagai commented 3 weeks ago

import rpy2.robjects as ro from rpy2.robjects.packages import importr import rpy2.robjects.packages as rpackages from rpy2.robjects import pandas2ri

def parse_CrossTalkeR(path):
    """
    Parameters
    ----------
    path: Location to the RDS object generated by CrossTalkeR 

    Returns
    -------
    tbldata : DataFrame Containing all the Results from CrossTalkeR

    Notes
    -----
    This algorithm was proposed in [1]_ and [2]_.

    """
    d = {'package.dependencies': 'package_dot_dependencies',
     'package_dependencies': 'package_uscore_dependencies'}
    ctker = importr('CrossTalkeR', 
                   robject_translations = d)
    readRDS = ro.r['readRDS']
    df = readRDS(path)
    phdat = df.slots['tables']
    tbldata = {}
    for i in enumerate(phdat.names):
        with (ro.default_converter + pandas2ri.converter).context():
            tbldata[i[1]] = pandas2ri.conversion.get_conversion().rpy2py(phdat[i[0]])
    return(tbldata)