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base repository: alexisvdb/singleCellHaystack
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head repository: alexisvdb/singleCellHaystack
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compare: haystack_refactor
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  • 2 commits
  • 2 files changed
  • 1 contributor

Commits on Sep 4, 2024

  1. Move code for comparing ranks to own function. Call that in plot_comp… 

    …are_ranks.
    @ddiez
    ddiez committed Sep 4, 2024
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  2. Push first version of the refactoring code. For now there is a new fu… 

    …nction call haystack_continuous_v2 that does the same as haystack_continuous_highD but calling mostly functions that do some of the stuff. Most of this is straitforward. The main differences are:

- Operations that can be done on regulare matrices or sparse matrices are encoded into function that recognize the matri type. This allows extending this approach to other matrix representations in the future, like maybe DelayedArray and IterableMatrix.

- Instead of calculating P and KLD for each gene in a go, we calculate a matrix P for each gene and grid point. This is passed to a function that calculates KLD. This gives identical results but permits to return the matrix P in the results if needed.

- During randomization before we would randomize each gene in each replication independently. Now we randomize all the columns in each replication. This is identical to what we do now in Python.
    @ddiez
    ddiez committed Sep 4, 2024
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