Misc

Hi,
I noticed that the vignette refers to uwot as github, but the package is officially on CRAN as you know.

cytofWorkflow/vignettes/cytofWorkflow.Rmd

Line 131 in 9762d03

    
           For visualization, we use new plotting functions from the `r Biocpkg("CATALYST")` package that employ `r CRANpkg("ggplot2")` as their graphical engine.  Notably, `r Biocpkg("CATALYST")` delivers a suite of useful visual representations of HDCyto data characteristics, such as an MDS (multidimensional scaling) plot of aggregated signal for exploring sample similarities.  The obtained cell populations are visualized using dimension reduction techniques (e.g., UMAP via the `r CRANpkg("umap")` package) and heatmaps (via the `r Biocpkg("ComplexHeatmap")` package [@Gu2016]) to represent characteristics of the annotated cell populations and identified biomarkers. (Note that an alternative R implementation of the UMAP algorithm with additional functionality is also available in the `r Githubpkg("jlmelville/uwot")` package.)

BTW, Burkhard Becher does not got any affiliation.
I didn't find why uwot is listed in the Depends of DESCRIPTION whereas it is not in the NAMESPACE.
Keep safe,
SAmuel

Great, thanks.

Just checked in a change to both release (3.11) and devel to fix the affiliation and the CRAN package link.

I think we put uwot in Depends, because it is needed by scater.