from pathlib import Path
import numpy as np
import pandas as pd
import GSForge as gsf

from rpy2.robjects import pandas2ri
%load_ext rpy2.ipython
pandas2ri.activate()

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
/tmp/ipykernel_5896/3198097203.py in <module>
----> 1 from rpy2.robjects import pandas2ri
      2 get_ipython().run_line_magic('load_ext', 'rpy2.ipython')
      3 pandas2ri.activate()

ModuleNotFoundError: No module named 'rpy2'

R Integration¶

#%%R
#suppressMessages({
#  library("sleuth")
#})

#%%R
#counts, labels = gsf.get_gem_data(agem, annotation_variables=['treatment', 'time', 'genotype'])
#labels = labels.to_dataframe()
#ri_counts = gsf.utils.R_interface.Py_counts_to_R(counts)

#%%R -i ri_counts -i dmatrix_list -i contrast_list -o results -o keep