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KasperSkytte / ampvis2

Tools for visualising microbial community amplicon data
https://kasperskytte.github.io/ampvis2/
GNU General Public License v3.0
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Cannot load the tree correctly #114

Closed Lei0509 closed 2 years ago

Lei0509 commented 3 years ago

Hi Kasper,

I cannot load my tree correctly using the following code: d <- amp_load(otutable = myasvtable,metadata = mymetadata,taxonomy = mytaxonomy,pruneSingletons = FALSE, tree = ape::read.tree("rootedtree.tree")) # read tree file

The error message is : Warning message: In ape::drop.tip(phy = tree, tip = tree$tip.label[!tree$tip.label %in% : drop all tips of the tree: returning NULL

When I run the code ape::read.tree("rootedtree.tree") . It return:

**Phylogenetic tree with 3538 tips and 3531 internal nodes. Tip labels: ae9fc5b50c57fb3773441edcef2f41b9, 076aa58034395275db0c802ffba3e75b, 6d98b5f71e38c20e6d061f8adbb55ea0, c106d7eda7af2b8c1c169dd1276284d7, 1c2078a5c4ee47a7575f11a3a40f37c1, 96acd73109395813e7a59335303f7188, ... Node labels: root, 1.000, 0.487, 0.969, , 0.995, ...

Rooted; includes branch lengths.**

Can you please help me to solve this issue?

Thank you so much for your help!

Best Regards, Lei

KasperSkytte commented 3 years ago

Hi there. To me it seems like you have loaded mismatching data. The tip labels of the tree don't match the names of the OTU's in the otutable. Check that first, and I'll gladly take a deeper look.