How do I select some of the many groupings for analyse and visualise in Taxonomic analysis

User Support
1

The commands are as follows:
time qiime taxa barplot
--i-table table.qza
--i-taxonomy taxo.qza
---m-metadata-file total/metadata.tsv
--o-visualisation taxa-bar-plots.qzv

I have way too many barcode groupings for my splits, it's an extremely rich library with 96 of them. At first I simply changed the metadata.tsv file to remove all the information about the groupings I didn't want to see, and then re-visualised as in the following command:

time qiime taxa barplot
--i-table table.qza
--i-taxonomy taxo.qza
---m-metadata-file total/metadata_STDI.tsv
--o-visualisation taxa-bar-plots.qzv

But I thought it was too simple.

Plugin error from taxa.
Sample IDs found in the table are missing in the metadata: {'1', '2', '3', ......} .
Debug info has been saved to /tmp/qiime2-q2cli-err-c_xbedhj.log

So that's my problem.

2

Good afternoon!

You can group samples together into larger groups, then just graph the groups with:
qiime feature-table group
https://docs.qiime2.org/2023.9/plugins/available/feature-table/group/

That function has a few settings to choose from, so try it out and let us know if you have questions!

3

@colinbrislawn
Thank you for your reply. I have used qiime feature-table group command but I still got this problem.

Command: qiime feature-table group
Data can only be summed or meaned or medianed through --p-mode TEXT Choices('mean-ceiling', 'median-ceiling', 'sum'). But what I want is to process only some of data in the metadata and delete the remainder that I dont process. I changed the metadata file, and deleted all the rows I wasnt interested in, and ran this command, as follows:

time qiime feature-table group
--i-table table_p.qza
--p-axis sample
--m-metadata-file total/Pmetadata_onlySTDI.tsv
--m-metadata-column barcodes
--p-mode sum
--o-grouped-table test.qza

Error message is:
Plugin error from feature-table:
The following IDs are not present in the metadata: '1', '2', ..., '96'
Debug info has been saved to /tmp/qiime2-q2cli-err-9wlx7mu4.log

He doesn't seem to allow me to not deal with rows that I don't want to deal with.

1 Like
4

This is correct. Here is how to do this:

First, group the table while including all samples (even the ones you don't want!)

Then, remove the samples you don't want with
https://docs.qiime2.org/2023.9/plugins/available/feature-table/filter-samples/

This is basically the same as you described:

But what I want is to process ~~only some of data in ~~the metadata and delete the remainder that I dont process [from the grouped table using filter-samples].

By the way, you can see a full list of built-in Qiime2 commands here.
I check this list often when I am trying to figure out how to do something new.

3 Likes
5

Amazing! Thanks for helping me with my problem. It's feeled good to see the document to solve my problem, I will try to continue to learn in the list of connections you provide, thanks!

1 Like