Problem with phylo tree in microtable creation

[martina-nasuelli]

Hello @ChiLiubio

Thanks for this great package!

I've just started using microeco a few days ago, but I'm encountering a problem with adding the phylo tree file to the microtable of my data.

I can perform all analyses if I exclude the phylo_tree option in the qiime2eco function, but when I try to add the tree file the package returns this error:

Error in self$tidy_dataset() :
No same feature name found among otu_table, tax_table and phylo_tree! Please check feature names in those objects!

The problem is that the tip.label of the tree file are the same in the first column of otu_table, as they are derived from the same analyses and qza files in QIIME2.

Do you have any suggestions on how to overcome this problem?

Thank you very much!

Martina

[ChiLiubio]

Hi @martina-nasuelli
Please make sure the row names of otu_table and tax_table are ASV names. Then please ensure that the row names of otu_table are same with the tip labels in the tree file (same format). For such error, a possible reason is the tip labels have some unexpected characters. You may need check it. If there are some characters that you donnot need, please delete them with the functions such as gsub

Best,
Chi

[martina-nasuelli]

Hello Chi, the row names of the otu and taxa table are ASV names (one example: AY496043.1.1552_U, named after QIIME2 closed-reference taxonomy assignation). The same names are found in the tree file. So I don't know what to do. what do you suggest? I also take the opportunity to ask you another question. I've tried to create a microtable from CSV files but I am encountering this issue: *Error in private$check_abund_table(otu_table) : Some columns in otu_table are not numeric class! Please check the input data!* I have this problem with both the CSVs from my data and the CSVs exported with the function save_table () from the data available in the microeco package. How can I overcome this problem? Thank you again for your help. Best regards, *Martina Nasuelli, *PhD student Università del Piemonte Orientale Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DiSSTE) Piazza Sant'Eusebio 5, 13100 - Vercelli, Italy Google Scholar <https://scholar.google.com/citations?hl=it&view_op=list_works&gmla=AJsN-F7yLKtw4EQIsjnfDMRSWzFmyF4E48O6LKKYsKLNV08MRAaezbKyZIVeZwdEvgWSd4-IHaEipDdykvftRsRxTOoB9XBWScIzsMYs5xaa-k21Fme9Sotb2Efe7Dt6_RfK1K9ey5WisciHR7W4GvHjF8Ct-gPvbA&user=NsdvzOIAAAAJ> ResearchGate <https://www.researchgate.net/profile/Martina-Nasuelli-2> Twitter <https://twitter.com/MNasuelli> Il giorno mer 20 nov 2024 alle ore 02:42 Chi Liu ***@***.***> ha scritto:

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Hi @martina-nasuelli <https://github.com/martina-nasuelli> Please make sure the row names of otu_table and tax_table are ASV names. Then please ensure that the row names of otu_table are same with the tip labels in the tree file (same format). For such error, a possible reason is the tip labels have some unexpected characters. You may need check it. If there are some characters that you donnot need, please delete them with the functions such as gsub Best, Chi — Reply to this email directly, view it on GitHub <#436 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJEVCRG6UZOEQC3I4NMUL4T2BPSH3AVCNFSM6AAAAABSCOSOVCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOBXGEZTQOJVHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[ChiLiubio]

Hi.
One way is to create microtable object with minimum data file first and try to add another one. Then we can identify which one caused the error.

library(microeco)
data(sample_info_16S)
data(otu_table_16S)
data(taxonomy_table_16S)
data(phylo_tree_16S)

test <- microtable$new(sample_table = sample_info_16S, otu_table = otu_table_16S)
test <- microtable$new(sample_table = sample_info_16S, otu_table = otu_table_16S, tax_table = taxonomy_table_16S)
test <- microtable$new(sample_table = sample_info_16S, otu_table = otu_table_16S, tax_table = taxonomy_table_16S, phylo_tree = phylo_tree_16S)

The second issue shows the otu_table is not numeric. Please check it again. If it is still there, please attach the data and steps that I can use to reproduce the issue. Thanks.

Best,
Chi

[martina-nasuelli]

Hello Chi, I am still encountering problems. I solved the problem with the numerical values. But again, I am finding myself dealing with name errors. When I start working with QIIME2 files, the problem is the names of the tip labels in the tree, an R return this error: Error in self$tidy_dataset() : No same feature name found among otu_table, tax_table and phylo_tree! Please check feature names in those objects! but everything else works fine and I can perform the analyses. But if I take the csv files exported from the QIIME2 file with the function save_table and trying to import them, the error is the following: Error in private$tidy_samples(self) : No same sample name found between rownames of sample_table and colnames of otu_table! Please first check whether the rownames of sample_table are sample names! Then check through the sample names of each table! But they derive from the QIIME2 files. The general problem is that the names of the otu columns, samples and tip labels are not coherent. I cannot find the root of the problem here. I've attached the script and the csv files I am using. Thank you again! Il giorno sab 23 nov 2024 alle ore 02:45 Chi Liu ***@***.***> ha scritto:

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Hi. One way is to create microtable object with minimum data file first and try to add another one. Then we can identify which one caused the error. library(microeco) data(sample_info_16S) data(otu_table_16S) data(taxonomy_table_16S) data(phylo_tree_16S) test <- microtable$new(sample_table = sample_info_16S, otu_table = otu_table_16S) test <- microtable$new(sample_table = sample_info_16S, otu_table = otu_table_16S, tax_table = taxonomy_table_16S) test <- microtable$new(sample_table = sample_info_16S, otu_table = otu_table_16S, tax_table = taxonomy_table_16S, phylo_tree = phylo_tree_16S) The second issue shows the otu_table is not numeric. Please check it again. If it is still there, please attach the data and steps that I can use to reproduce the issue. Thanks. Best, Chi — Reply to this email directly, view it on GitHub <#436 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJEVCRH527UH3MHD2OUO5NL2B7M2DAVCNFSM6AAAAABSCOSOVCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOJVGIYDANBTGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[ChiLiubio]

Hi. It seems like that data cannot be attached with email. Please check it.

[martina-nasuelli]

Hi Chi, Here are the data files. Thank you. Regards, *Martina Nasuelli* Il giorno dom 24 nov 2024 alle ore 10:01 Chi Liu ***@***.***> ha scritto:

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Hi. It seems like that data cannot be attached with email. Please check it. — Reply to this email directly, view it on GitHub <#436 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJEVCRG5IKB2EMFMX4KFQID2CGIWNAVCNFSM6AAAAABSCOSOVCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOJVHA3TSNRWHE> . You are receiving this because you were mentioned.Message ID: ***@***.***>