Closed csoneson closed 4 years ago
Now, say we have a different dimensionality reduction approach which has not yet been implemented with SingleCellExperiment objects in mind. For example, let's say we want to explicitly use the
umap()
function as implemented in theuwot
package.
Seems like the original text was wrong, we have runUMAP
that does exactly this.
Seems like the original text was wrong, we have runUMAP that does exactly this.
Yes; my attempt was to make a minimal change that would still illustrate the general approach, but remove the statement about scater
using umap
. But it's of course true that uwot::umap
has already been implemented with SingleCellExperiment objects in mind...
@robertamezquita merge and fix re. my comment above.
Re: chosen
in the data integration chapter: it is mentioned on lines 209 and 223, but never initialized and never used. Fix depends on whether the intention was to use a subset of the genes or not - if yes, I guess these two mentions should be changed to chosen.hvgs
and an argument subset.row
provided on lines 217-218; if not, those text lines should be modified.
Addresses most of the points mentioned in #7