muon 0.1.0

muon is a multimodal omics Python framework.

Data structure

In the same vein as scanpy and AnnData are designed to work with scRNA-seq data in Python, muon and MuData are designed to provide functionality to load, process, and store multimodal omics data.

MuData
  .obs     -- annotation of observations (cells, samples)
  .var     -- annotation of features (genes, genomic loci, etc.)
  .obsm    -- multidimensional cell annotation, 
              incl. a boolean for each modality
              that links .obs to the cells of that modality
  .varm    -- multidimensional feature annotation, 
              incl. a boolean vector for each modality
              that links .var to the features of that modality
  .mod
    AnnData
      .X    -- data matrix (cells x features)
      .obs  -- cells metadata (assay-specific)
      .var  -- annotation of features (genes, peaks, genomic sites)
      .obsm
      .varm
      .uns
  .uns

By design, muon can incorporate disjoint multimodal experiments, i.e. the ones with different cells having different modalities measured. No redundant empty measurements are stored due to the distinct feature sets per assay as well as distinct cell sets mapped to a global set of observations.

Input

For reading multimodal omics data, muon relies on the functionality available in scanpy. muon comes with MuData — a multimodal container, in which every modality is an AnnData object:

from muon import MuData

mdata = MuData({'rna': adata_rna, 'atac': adata_atac})

If multimodal data from 10X Genomics is to be read, muon provides a reader that returns a MuData object with AnnData objects inside, each corresponding to its own modality:

import muon as mu

mu.read_10x_h5("filtered_feature_bc_matrix.h5")
# MuData object with n_obs × n_vars = 10000 × 80000 
# 2 modalities
#   rna:	10000 x 30000
#     var:	'gene_ids', 'feature_types', 'genome', 'interval'
#   atac:	10000 x 50000
#     var:	'gene_ids', 'feature_types', 'genome', 'interval'
#     uns:	'atac', 'files'

I/O with .h5mu files

muon operates on multimodal data (MuData) that represents modalities as collections of AnnData objects. These collections can be saved to disk and retrieved using HDF5-based .h5mu files, which design is based on .h5ad file structure.

mdata.write("pbmc_10k.h5mu")
mdata = mu.read("pbmc_10k.h5mu")

It allows to effectively use the hierarchical nature of HDF5 files and to read/write AnnData object directly from/to .h5mu files:

adata = mu.read("pbmc_10k.h5mu/rna")
mu.write("pbmc_10k.h5mu/rna", adata)

Multimodal omics analysis

muon incorporates a set of methods for multimodal omics analysis. These methods address the challenge of taking multimodal data as their input. For instance, while for a unimodal analysis one would use principal components analysis, muon comes with a method to run multi-omics factor analysis:

# Unimodal
import scanpy as sc
sc.tl.pca(adata)

# Multimodal
import muon as mu
mu.tl.mofa(mdata)

Individual assays

Individual assays are stored as AnnData object, which enables the use of all the default scanpy functionality per assay:

import scanpy as sc

sc.tl.umap(mdata.mod["rna"])

Typically, a modality inside a container can be referred to with a variable to make the code more concise:

rna = mdata.mod["rna"]
sc.pl.umap(rna)

Modules in muon

muon comes with a set of modules that can be used hand in hand with scanpy's API. These modules are named after respective sequencing protocols and comprise special functions that might come in handy. It is also handy to import them as two letter abbreviations:

# ATAC module:
from muon import atac as ac

# Protein (epitope) module:
from muon import prot as pt