Unimodal omics

muon enhances efficiency and user experience when analysing individual omics by offering general functions for processing and plotting count data as well as functionality crafted for individual omics such as chromatin accessibility or antibody-derived tags. Omic-specific functions are grouped into respective modules inside muon.

• ATAC-seq
  • Quality control
    • Nucleosome signal
    • TSS enrichment
  • Normalisation
  • Differentially accessible peaks
  • Gene activity
• CITE-seq
  • Normalisation
    • dsb
    • CLR

In-place filtering

When subsetting AnnData objects with scanpy.pp.filter_cells() / scanpy.pp.filter_genes(), the AnnData object is being copied. Using the slicing syntax (e.g. adata[cell_ids]) results in a View object, which has to be copied then for any modidying operations. While this behaviour can be useful in many cases, that nearly doubles the amount of required memory and introduces unnecessary challenges when handling exceptionally large datasets.

muon introduces functions for in-place filtering: muon.pp.filter_obs() and muon.pp.filter_var(). These function directly modify the AnnData object that they are called on. Their syntax allows them to also be more general than the aforementioned filtering functions.

mu.pp.filter_obs(adata, 'total_counts', lambda x: (x >= 10000) & (x <= 50000))
# This is analogous to
#   sc.pp.filter_cells(atac, min_counts=10000)
#   sc.pp.filter_cells(atac, max_counts=50000)
# but does in-place filtering avoiding copying the object

In-place filtering functions also accept names of observations or variables to be subsetted as well as boolean vectors.

obs_names_subset = ['AAACAGCCAATCCCTT-1', 'AAACAGCCAATGCGCT-1', ...]
mu.pp.filter_obs(adata, obs_names_subset)

adata.var.include_feature.values.dtype.name
# => 'bool'
mu.pp.filter_var(adata, adata.var.include_feature.values)

In-place filtering is not defined for views. On backed objects, it has to be used with care: data for the requested subset of .X will be read into memory and the object will not be backed anymore.

Histograms

In the same way as violin plots created with scanpy.pl.violin() are used to visualise quality control steps, muon.pl.histogram() allows to plot histograms for continuous measurements across cells:

mu.pl.histogram(adata, ['n_counts', 'n_genes'])

It can also be called on the muon.MuData object in the same way.