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select one modality after subsetting mudata by var (or obs) #32

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bio-la opened this issue Dec 9, 2022 · 1 comment
Closed

select one modality after subsetting mudata by var (or obs) #32

bio-la opened this issue Dec 9, 2022 · 1 comment
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enhancement New feature or request
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@bio-la
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bio-la commented Dec 9, 2022

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"]
@bio-la bio-la added the enhancement New feature or request label Dec 9, 2022
@gtca gtca added this to the 0.2.2 milestone Jan 8, 2023
@gtca gtca closed this as completed in 359d198 May 26, 2023
@gtca
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gtca commented May 26, 2023

Hey @bio-la,

Thanks for discovering this, and sorry it took a while to be fixed.
There was a bug in subsetting indeed but now it should be resolved.

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