Convert factors to pd.Categorical (#41)

anndata2ri/py2r.py

@@ -8,10 +8,10 @@
 from rpy2.robjects.conversion import localconverter
 from rpy2.robjects.vectors import ListVector
 from rpy2.robjects.methods import RS4
-from rpy2.robjects.packages import importr
 
 from . import conv_name
 from .conv import converter, mat_converter, full_converter
+from .rpy2_ext import importr
 
 
 class NotConvertedWarning(Warning):

anndata2ri/r2py.py

@@ -4,13 +4,13 @@
 from anndata import AnnData
 
 from rpy2.rinterface import NULLType, SexpS4
-from rpy2.robjects import default_converter
+from rpy2.robjects import default_converter, pandas2ri
 from rpy2.robjects.conversion import localconverter
 from rpy2.robjects.robject import RSlots
-from rpy2.robjects.packages import importr
 
 from . import conv_name
 from .conv import converter, mat_converter, full_converter
+from .rpy2_ext import importr
 from .scipy2ri import supported_r_matrix_classes
 from .scipy2ri.r2py import rmat_to_spmat
 
@@ -35,7 +35,7 @@ def rpy2py_data_frame(obj: SexpS4) -> pd.DataFrame:
     """
     S4 DataFrame class, not data.frame
     """
-    with localconverter(default_converter):
+    with localconverter(default_converter + pandas2ri.converter):
         slots = RSlots(obj)
         columns = dict(slots["listData"].items())
         rownames = slots["rownames"]

anndata2ri/rpy2_ext.py

@@ -0,0 +1,18 @@
+from functools import lru_cache
+from typing import Optional, Union
+
+from rpy2.robjects import packages, Environment
+
+
+@lru_cache()
+def importr(name: str) -> packages.Package:
+    return packages.importr(name)
+
+
+@lru_cache()
+def data(package: str, name: Optional[str] = None) -> Union[packages.PackageData, Environment]:
+    if name is None:
+        return packages.data(importr(package))
+    else:
+        # Use cached version of PackageData collection and just fetch
+        return data(package).fetch(name)

anndata2ri/scipy2ri/py2r.py

@@ -6,9 +6,10 @@
 from rpy2.robjects import default_converter, numpy2ri, baseenv
 from rpy2.robjects import Vector, BoolVector, IntVector, FloatVector
 from rpy2.robjects.conversion import localconverter
-from rpy2.robjects.packages import importr, Package
+from rpy2.robjects.packages import Package
 from scipy import sparse
 
+from ..rpy2_ext import importr
 from .conv import converter
 
 

tests/test_py2rpy.py

@@ -6,9 +6,9 @@
 import scanpy as sc
 from anndata import AnnData
 from rpy2.robjects import baseenv, globalenv
-from rpy2.robjects.packages import importr
 
 import anndata2ri
+from anndata2ri.rpy2_ext import importr
 from anndata2ri.test_utils import conversions_py2rpy
 
 

tests/test_rpy2py.py

@@ -2,15 +2,15 @@
 import pandas as pd
 from anndata import AnnData
 from rpy2.robjects import r, conversion
-from rpy2.robjects.packages import importr, data
 
 import anndata2ri
+from anndata2ri.rpy2_ext import importr, data
 from anndata2ri.test_utils import conversions_rpy2py
 
+as_ = getattr(importr("methods"), "as")
 se = importr("SummarizedExperiment")
 sce = importr("SingleCellExperiment")
-sc_rna_seq_data = data(importr("scRNAseq"))
-as_ = getattr(importr("methods"), "as")
+sumex_allen = data("scRNAseq", "allen")["allen"]
 
 
 def check_allen(adata):
@@ -23,7 +23,6 @@ def check_example(adata):
     assert adata.obsm["X_pca"].shape == (100, 5)
 
 
-sumex_allen = sc_rna_seq_data.fetch("allen")["allen"]
 code_example = """
 local({
     ncells <- 100
@@ -60,3 +59,16 @@ def test_convert_empty_df_with_rows(convert):
 
     df_py = convert(anndata2ri, lambda: conversion.rpy2py(df))
     assert isinstance(df_py, pd.DataFrame)
+
+
+@pytest.mark.parametrize("convert", conversions_rpy2py)
+def test_convert_factor(convert):
+    code = """
+    SingleCellExperiment::SingleCellExperiment(
+        assays = list(counts = matrix(rpois(6*4, 5), ncol=4)),
+        colData = S4Vectors::DataFrame(a_factor = factor(c(rep('A', 3), rep('B', 1))))
+    )
+    """
+    ad = convert(anndata2ri, lambda: r(code))
+    assert isinstance(ad.obs["a_factor"].values, pd.Categorical)
+    assert all(ad.obs["a_factor"].values == pd.Categorical.from_codes([0, 0, 0, 1], ["A", "B"]))

tests/test_scipy_rpy2py.py

@@ -5,10 +5,10 @@
 import pytest
 from rpy2.rinterface import Sexp
 from rpy2.robjects import baseenv, r, numpy2ri
-from rpy2.robjects.packages import importr
 from scipy import sparse
 
 from anndata2ri import scipy2ri
+from anndata2ri.rpy2_ext import importr
 from anndata2ri.test_utils import conversions_rpy2py, ConversionModule