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Programming philosopy

BPCells operates according to a somewhat different programming philosophy from other tools. In particular:

  • BPCells aims to perform most analysis directly from raw data matrices or aligned fragments
    • It does not modify input data files, instead preferring to write a copy to a new location when needed.
    • Analysis code that runs quickly from raw counts provides clear reproducibility and data provenance
  • BPCells generally avoids storing normalized matrix copies (sometimes referred to as layers), instead preferring to re-calculate normalized values on-the-fly. This helps to avoid wasteful storage use.
  • BPCells does not (currently) have a concept of a “project” object that combines data + metadata in a complex structure.

Working without a project object

Imagine you want to plot a UMAP of your cells colored by cluster. In BPCells, the way you do this is by providing:

1, The matrix of cells x UMAP coordinates 2. A vector listing which cells belong to which cluster

The correspondence of cells and clusters is determined based on ordering. So the rows of the UMAP matrix should have the same order as the cluster membership vector.

To keep this simple, we recommend the following approach:

  1. At the start of your analysis, establish a consistent cell ordering when you perform quality filtering
    • See the tutorial for an example, where we make a keeper_cells vector and order our data consistently according to that list of cell IDs.
  2. For all downstream operations (PCA, clustering, etc.), this cell order will be preserved unless you explicitly change it. So things will “just work”
  3. To keep track of per-cell metadata, it can be helpful to make a data frame tracking sample IDs, cluster membership, and other metadata yourself

Working without a project object provides a lot of flexibility, since as the user you can easily swap UMAP embeddings, cluster assignments, etc. by just providing a different variable as input. There’s also no need to “export” your metadata since there wasn’t an import step to begin with.

Of course, this power does come with additional responsibility to keep track of metadata. Keeping BPCells flexible for power users while retaining ease-of-use for newbies is an ongoing effort, but BPCells currently falls more on the side of power users