Missing taxa names after exporting taxa plot data

Hello,
I have been able to get and view my taxa plot. I use the “Download CSV” button on the web page to try and get the absolute taxa abundance into excel. However, after doing this I realise some of the rows (which have the taxa) do not have taxa labels but the abundances are there on the table.

Can anyone help me solve this. Thanks!

Jewelna

Hi @Jewelna_Osei-Poku,
I’m not sure exactly what you’re talking about. Including the commands you’ve run, and/or some screen captures would help.

If you’re talking about the download CSV button on taxa-bar-plot Visualization…

… I think there may be some confusion. I believe the rows in that CSV are Sample IDs, not feature IDs.

It’s not unexpected to have some features that are not assigned a taxonomy - no database has every sequence in it, after all.

Hope this helps. If not, feel free to post a more detailed question.

Chris :snake:

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Hello Chris,
Kindly find attached a screenshot of part of the excel sheet with truncated taxa names.

@Jewelna_Osei-Poku, what visualization did you get that from? In other words, what command did you run to produce the viz?

@ChrisKeefe: I run the command below:
caffeinate qiime feature-classifier classify-sklearn --i-classifier SILVA132_99_classifier.qza --i-reads rep-seqs-nonchimeric.qza --o-classification taxonomy-nonchimeric.qza

qiime taxa barplot --i-table table-nonchimeric.qza --i-taxonomy taxonomy-nonchimeric.qza --m-metadata-file hkwm_metadata.tsv --o-visualization taxa-bar-plots_sklearn.qzv

qiime tools view taxa-bar-plots_sklearn.qzv

I got the bar plots okay (see attached screenshot). Then I click on CSV to get the data which I copy and past in Excel. And the result table is what I get.
Screenshot 2020-11-18 at 8.05.13 PM|690x363 )

I’m sorry, @Jewelna_Osei-Poku, but I’ve been unable to reproduce your issue. All I can think of is that maybe the problem occurs when you

You might try opening the file with Excel instead. (I just use the Open With option when downloading, pictured below). Using a plain text editor or programming language like Python or R to look at the .tsv immediately after downloading might be even better. Spreadsheet software is powerful, but sometimes it does bad things to data when it’s trying to help.

If that doesn’t work, would you feel comfortable sharing your taxa-bar-plots_sklearn.qzv and the tsv it produces? You can do that here, or by private message if that’s better for you. I’d like to try to reproduce your error on this machine, and maybe take a look at the provenance if I can get it to repeat the issue.

Best,
Chris

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@ChrisKeefe: You were right. It was the copy and past that was the problem. I simply ‘Saved As’ an .csv after clicking the CSV tab, and it was fine. Thanks for the help. Much appreciated.

Jewelna

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