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grunwaldlab / metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
http://grunwaldlab.github.io/metacoder_documentation
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deseq2 branch #325

Closed sghignone closed 2 years ago

sghignone commented 2 years ago

Hi Zach! I'm a user of the dev deseq2 branch but it's not working since the release of the master v3.5 -- I guess--. When I install the dev branch with devtools::install_github("grunwaldlab/metacoder", ref = "deseq2") I get installed the v3.4. With this version, the function: ( obj <- metacoder::parse_phyloseq(phyloseq) ) is not working, and I get the error Error: 'ranks_ref' is not an exported object from 'namespace:taxa'. To over come this, I install the master version, and the function works, but at this point, metacoder::calc_diff_abund_deseq2 is not working (obviously, Error: 'calc_diff_abund_deseq2' is not an exported object from 'namespace:metacoder'). Once I've installed the dev branc, I can prepare the obj for the graphical output, but when I run 

obj %>%
  taxa::filter_taxa(taxon_ranks == "Order", supertaxa = TRUE) %>%
  heat_tree(node_label = taxon_names,
            node_size = n_obs, [...]

I get Error: 'filter_taxa' is not an exported object from 'namespace:taxa'

I think syncro with current taxa should be revised. Thanks,

zachary-foster commented 2 years ago

Hello,

Thanks for the info. The calc_diff_abund_deseq2 function has been recently move to the primary development branch, so it can be insatlled with just:

devtools::install_github("grunwaldlab/metacoder")

The other issue is that the old version of taxa has been reintegrated into metacoder until I can finish updaing the new version of taxa (we could not have both versions on CRAN at once and metacoder needed to be updated, so this is temporary fix). Therefore the code should be: 

obj %>%
  metacoder::filter_taxa(taxon_ranks == "Order", supertaxa = TRUE) %>%
  heat_tree(node_label = taxon_names,
            node_size = n_obs, [...]

Does that solve the problems?

sghignone commented 2 years ago

sorted! Thanks

zachary-foster commented 2 years ago

Thanks!

I just installed it with:

devtools::install_github("grunwaldlab/metacoder")

and was able to see calc_diff_abund_deseq2. Can you try installing it again and if you still have the problem include your sessionInfo()

davidoctaviobotero commented 2 years ago

Hi Zach,

Thank you for the early response. I deleted the issue. Yes, now I can see the function.

Best,