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Software design

Source: vignettes/software_design.Rmd
software_design.Rmd

anndataR is designed to offer the combined functionality of the following packages:

  • theislab/zellkonverter: Convert AnnData files to/from SingleCellExperiment objects.
  • mtmorgan/h5ad: Read/write *.h5ad files natively using rhdf5.
  • dynverse/anndata: An R implementation of the AnnData data structures, uses reticulate to read/write *.h5ad files.

Ideally, this package will be a complete replacement for all of these packages, and will be the go-to package for working with AnnData files in R.

Desired feature list

  • Provide an R6 class to work with AnnData objects in R (either in-memory or on-disk).
  • Read/write *.h5ad files natively
  • Convert to/from SingleCellExperiment objects
  • Convert to/from Seurat objects

Class diagram

Here is a diagram of the main R6 classes provided by the package:

Notation:

  • X: Matrix - variable X is of type Matrix
  • *X: Matrix - variable X is abstract
  • as_SingleCellExperiment(): SingleCellExperiment - function as_SingleCellExperiment returns object of type SingleCellExperiment
  • *as_SingleCellExperiment() - function as_SingleCellExperiment is abstract