Improve use of log1p in the single-cell vignette

[pcarbo]

@stephens999 wrote:

In the single cell vignette we use log1p directly, rather than something that preserves the sparsity of the matrix.
And we note the potential to do this in a smarter way.

I think we should change it so that we actually work with sparse matrices, so that the code will work even for
larger problems. In practice I think people will just copy the code without necessarily reading the note.