Why has GNEISS been deprecated from Qiime2?

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Hi @ecg, thank you for your interest in gneiss.

Gneiss has not been deprecated -- only some of the visualizers have been deprecated in favor of Empress. By the next release, there will be compatibility between Songbird (possibly Aldex2) and Gneiss, where the ILR transform can be applied directly to differential abundance analysis results.

Of course, there will be more features coming up in the future (hence the FeatureTensor discussion)
See the following pull requests.

Regarding your questions

  1. gneiss_hierarchy.qza can export a newick file, which can be read into R. See Exporting data — QIIME 2 2019.10.0 documentation
  2. gneiss_heatmap.qzv, this probably can't be ported into R, but there are a number of tools that support phylogenetic heatmaps in R. See for instance phylo.heatmap: Creates a phylogenetic heat map in phytools: Phylogenetic Tools for Comparative Biology (and Other Things)
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