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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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DEICODE #1259

Open hollylutz opened 4 years ago

hollylutz commented 4 years ago

Hi Joey,

Do you have any plans to incorporate Cameron Martino's DEICODE method into the ordinate function of phyloseq? As I've only really worked with phyloseq, I am not sure how to get the results from my analyses with DEICODE (the distance matrix) back into R where I can make my own PCoA plots. Usually I just use the ordinate function with my ps object and go from there.

e.g. what I usually do with phyloseq...

ps.unif.log = ordinate(ps, method = "PCoA", distance = "unifrac") ps.unif.evals = ps.unif.log$values$Eigenvalues p = plot_ordination(ps, ps.dist.unif.log, color="thing") + coord_fixed(sqrt(ps.dist.unif.evals[2] / ps.dist.unif.evals[1]))

I guess I can use something like the eigen function in R to get eigenvalues, but I'm not sure what exactly is going into the ps.log file produced by the ordinate function.

Thanks in advance, Holly

spholmes commented 4 years ago

Hi Holly If you look at Chapter 9 of the book with WOlfgang there are all the different ways you can get ordination plots in R from a distance matrix, you don't need phyloseq for that Here is a link : http://web.stanford.edu/class/bios221/book/Chap-MultivaHetero.html

Best Susan

On Tue, Nov 5, 2019 at 8:16 AM hollylutz notifications@github.com wrote:

Hi Joey,

Do you have any plans to incorporate Cameron Martino's DEICODE https://forum.qiime2.org/t/robust-aitchison-pca-beta-diversity-with-deicode/8333 method into the ordinate function of phyloseq? As I've only really worked with phyloseq, I am not sure how to get the results from my analyses with DEICODE (the distance matrix) back into R where I can make my own PCoA plots. Usually I just use the ordinate function with my ps object and go from there.

e.g. what I usually do with phyloseq...

ps.unif.log = ordinate(ps, method = "PCoA", distance = "unifrac") ps.unif.evals = ps.unif.log$values$Eigenvalues p = plot_ordination(ps, ps.dist.unif.log, color="thing") + coord_fixed(sqrt(ps.dist.unif.evals[2] / ps.dist.unif.evals[1]))

I guess I can use something like the eigen function in R to get eigenvalues, but I'm not sure what exactly is going into the ps.log file produced by the ordinate function.

Thanks in advance, Holly

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