Changelog • spatialDWLS

spatialDWLS 0.1.1

A cluster label with no spots in the expression no longer stops the run with “quadratic program could not be solved”. Named clusters may now be a superset, e.g. the clusters of a whole dataset when expr is a subset.
In a cluster with a single candidate cell type, a spot with no signal on the signature features is now NA, as it is in every other cluster; it was returned as proportion 1 of that type.
dwls_stream() matches the second round’s spots to the first round’s by name, so a read_window() that returns a window’s spots in a different order on a later pass no longer gives silently wrong results.
Duplicated or missing cell type names, feature names or spot IDs are now an error; a duplicated cell type silently overwrote another’s proportions. NA clusters get an error that says so.
Parallel runs no longer send every task’s expression slice to each worker.

Noted for 0.1.0: the PAGE step that picks candidate cell types reverse-logs with logbase. Giotto <= 4.3.1 used base 2 there whatever logbase was, so results differ from it slightly for logbase other than 2 (identical at the default).

First release as a standalone package. The algorithm was previously runDWLSDeconv() inside Giotto (<= 4.3.1), which now calls this package.

Results match Giotto 4.3.1 to floating point (~1e-15), except where these bugs were fixed:

Clusters with a single candidate cell type in the spot round now assign that type proportion 1; they were left at 0.
Small negative values from the constrained solver are now clipped to 0 for every cell type, not only the last one.
Running DWLS no longer leaves the session’s random number generator in a fixed state.

Faster (12-22x serial on 600-20,000 spots):

The dampening constant’s cross-validation uses .lm.fit() on k x k weighted least squares instead of lm(), and draws its 100 subsets once.
Weighted solves use crossprod(S * w, S) instead of a features x features diag(w), and call Matrix::nearPD() only when the matrix needs it.
The reverse-log transform keeps sparse input sparse and touches only the signature features.

New:

BPPARAM for parallel per-cluster plans and per-spot solves.
dwls_stream() for expression read in windows.
na_as_zero.
dwls_signature(), the matrix form of Giotto’s makeSignMatrixDWLSfromMatrix().