Hi!
I noticed a bug when selecting a subset of genes in all layers of a mudata object created with the axes=-1 convention.
The subsetting works fine, but if i try to select one modality in the selected feature subset, it's not working ( i will open a functionality request too)
However after this error i can't subset the mudata object again - something gets updated in the object that prevents the normal functionality.
minimal example below.
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"]
mdata[:,mdata.var_names.str.startswith("MT-")]
Hi! I noticed a bug when selecting a subset of genes in all layers of a mudata object created with the
axes=-1
convention. The subsetting works fine, but if i try to select one modality in the selected feature subset, it's not working ( i will open a functionality request too) However after this error i can't subset the mudata object again - something gets updated in the object that prevents the normal functionality. minimal example below. thanks!