select one modality after subsetting mudata by var (or obs) #32
Description
Hello!
I would like to be able to select a mudata layer after subsetting the object by var (or by obs). However, this is currently not implemented and it also breaks the mudata object (see issue #31 )
minimal example below, last line is the functionality i would like to have that breaks the mudata.
thanks!
import scanpy as sc
import mudata as md
from mudata import MuData
import anndata as ad
import numpy as np
import pandas as pd
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
np.random.seed(1979)
import mudatasets as mds
mds.list_datasets()
mds.info('pbmc5k_citeseq')
pbmc5k=mds.load('pbmc5k_citeseq',files=['filtered_feature_bc_matrix.h5'])
pbmc5k
rna_raw = pbmc5k["rna"].copy()
rna_raw.var_names_make_unique()
rna_a = rna_raw[np.sort(np.random.choice(np.arange(300), 300, replace=False)),:].copy()
rna_b = rna_raw[np.sort(np.random.choice(np.arange(700), 500, replace=False)),:].copy()
mdata = MuData({"raw": rna_raw, "preproc_1": rna_a, "preproc_2": rna_b}, axis=-1)
mdata[:,mdata.var_names.str.startswith("MT-")]
mdata[:,mdata.var_names.str.startswith("MT-")]["preproc_1"]