Refactor #10
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Refactor #10
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Plan: - make Salamander compatible with anndata - reimplement NMF models one at a time Remove all algorithms except KL-NMF. The goal is to avoid having a broken software along the refactorization.
The plotting module is now implemented around AnnData objects. Computation and plotting is separated into the tools and plot modules. One major change is that samples now correspond to rows instead of columns of the mutation count matrix.
Samples now correspond to rows. The variable names are adapted to fit the new plotting module.
Function names now include the names of the input data type if there are multiple versions, e.g., an implementation for numpy arrays and a wrapper around this implementation for AnnData inputs.
n_components is now an explicit argument of the dimensionality reduction. The motivation was to improve the transparency of the code.
A joint dimensionality reduction of multidimensional observation annotations of multiple anndata objects is useful for models with shared embedding spaces, e.g. (multimodal) correlated NMF.
no longer support
The KL-NMF implementation now only supports the faster joint update rules.
update the KL-NMF tests to the AnnData based model structure
The function 'get_obs_order' is necessary for the multimodal exposure plot and should therefore not be private.
The new implementation of multimodal correlated NMF doesn't use the 'add_penalty' parameter
This reverts commit 5081d62.
The scatter and embedding plot now have color and zorder options. This is useful for plotting multiple subgroups of points, e.g., the signature and sample embeddings in correlated NMF.
Add functions to plot .obs and .obsm attributes of multiple AnnData and MuData objects.
Add color and zorder options to the embedding plot. I also removed the abstraction of the embedding plot in signature_nmf to improve the readability of the code.
Implemented modality-specific updates to improve the indentation and readability.
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Refactor Salamander using the AnnData and MuData data structures.