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PhyloRPCA qurro outputs - download node Taxon IDs? #107

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callaband opened this issue Dec 10, 2024 · 5 comments
Open

PhyloRPCA qurro outputs - download node Taxon IDs? #107

callaband opened this issue Dec 10, 2024 · 5 comments

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@callaband
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phyloRPCA best describes my data, so wanted to use qurro to get ranked feature lists. Everything works the way it is supposed to, no errors there.

However, the top differentially ranked items from phyloRPCA include node ids (n###), which are unable to be merged with the gg2 taxonomy (G00####). However, I see that the node has a name in the qurro Taxon display. Is there a way to export the Taxon info with the download selected features button?

One example: I go from 92 of the top differentially ranked features to only 30 with annotated names

Parsing the tree myself seems time intensive. I supposed I could copy and paste, but was avoiding doing a repetitive manual task.

@cameronmartino
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Hi @callaband,

Maybe I am misinterpreting the question but there should be a phylo-taxonomy.qza (if using QIIME2) or t2t-taxonomy.tsv if using the standalone CLI which should provide the lowest common ancestor taxonomy for all internal nodes. That taxonomy should be (at least as much as possible) fully filled in and can be used inn Qurro.

Does that answer you question?

@callaband
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Oh my gosh, I didn't realize it was different from my other taxonomy file and hadn't noticed that the nodes were present in it. Thank you, that makes it much easier!

Related, is there a way to use ranked features for a subset of the data on the full table like you can with RPCA? I tried using the subset ordination file, full phyloRPCA table, then tried both full and subset taxonomy files - but there seemed to be a disconnects. Seemed to be that there were a bunch of features not present (nodes? It just said 2,345 features of the 9,456 ranked features not present). Basically I want to see if top ranked features at the end of the study generalize to the rest of the study.

@cameronmartino
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No problem. Similar to the taxonomy there is a table that is output from phylo-RPCA that should be used with Qurro. It exposes the internal nodes (sum of all the tips under it) as features in the table so that Qurro can use them for the ratios.

@callaband
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So is it end timepoint subset ordination/ranks, full table phyloRPCA output feature table - full table so I can see how the log ratio of subset ranked features looks at other timepoints, and subset taxonomy file?

I think that might error since the output from the full table might not have the same internal nodes of importance as the subset that then get put in the phyloRPCA output tables? Ignore the error and only look at features (OGU and/or nodes) in common?

@cameronmartino
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You need to use the same output tree and table from a signle phylo-RPCA they are matched at all internal nodes. If you use the input or the output tree from a separate run of phylo-RPCA they most likely will not match.

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