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microsud / microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages.
https://microsud.github.io/microbiomeutilities/
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Phy_tree not included in the result of format_to_besthit #173

Closed tcrispino13 closed 3 years ago

tcrispino13 commented 3 years ago

Is there a way to include the phy_tree in the phyloseq object after using the format_to_besthit function? Ive been following this commands and I need to measure the unifrac distances based on the phylogenetic tree but after using the format_to_besthit, it turns out the phy_tree was not included.

ps2 <- tax_glom(ps, "genus") ps2f <- format_to_besthit(ps) orddi <- ordinate(ps2f, method = "PCoA", distance = "unifrac", weighted= FALSE) Error in access(physeq, "phy_tree", errorIfNULL) : phy_tree slot is empty.

microsud commented 3 years ago

Hi @tcrispino13 Thanks for pointing this out. I will try to work on this when I have time, hopefully sometime this week or later next week.

Best wishes, Sudarshan

microsud commented 3 years ago

This is now fixed in #174 I will close the issue here.