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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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export for ITOL #730

Open dridk opened 7 years ago

dridk commented 7 years ago

http://itol.embl.de/help.cgi is an awesome website to plot tree with metadata. I m trying to export phyloseq object to a file which can be read by ITOL.

What's the best way ? Is there any way to export phyloseq object ?

spholmes commented 7 years ago

That interface supports newick format, all you need to do is use the ape function and write.newick of the tree component from your phyloseq object:

from https://github.com/joey711/phyloseq/issues/599

tree1 = phy_tree(physeq1)

ape::write.tree(tree1, "~/path/to/new/tree1.tree")

On Fri, Mar 17, 2017 at 8:48 AM, sacha schutz notifications@github.com wrote:

http://itol.embl.de/help.cgi is an awesome website to plot tree with metadata. I m trying to export phyloseq object to a file which can be read by ITOL.

What's the best way ? Is there any way to export phyloseq object ?

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dridk commented 7 years ago

Ok. It seems there are other format where metadata can be embeded. Any idea ?