# Abundances of taxa by group
**URL:** https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208
**Category:** User Support
**Tags:** heatmap
**Created:** [September 27, 2018, 1:11pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208 "2018-09-27T13:11:26Z")
**Posts on this page:** 14
**Page:** 1
### Author:  [@alfanon](https://forum.qiime2.org/u/alfanon)
#### Post date: [September 27, 2018, 1:11pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/1 "2018-09-27T13:11:27Z")
Dear all,
I am trying to create a table with the abundances (or relative abundances) of taxa at different taxonomic levels (phylum, family, genus) from my feature table, where the abundances are given not by sample, rather by a category from my metadata file, for example by Sample type. Is this possible or do I need to do it manually summing up the abundances of each sample for that category?
I know that I can use qiime taxa collapse first to collapse at the level I want, but then I don't know what to do.
A question related to this one is: do you advise to present in a publication the taxonomic barplots and the type of tables I would like to generate which are built from the rarefied feature table or from the complete table?
Thanks a lot in advance
Best wishes
Niccolò
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [September 27, 2018, 1:59pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/2 "2018-09-27T13:59:11Z")
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [September 27, 2018, 10:57pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/3 "2018-09-27T22:57:30Z")
Hey there @alfanon!
> [@alfanon](#):
>
> rather by a category from my metadata file
You're in luck! Check out [`feature-table group`](https://docs.qiime2.org/2018.8/plugins/available/feature-table/group/) for a way to regroup your feature table based on sample or feature metadata.:qiime2: 🦖
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [September 27, 2018, 10:57pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/4 "2018-09-27T22:57:32Z")
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### Author:  [@alfanon](https://forum.qiime2.org/u/alfanon)
#### Post date: [September 28, 2018, 8:27am UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/5 "2018-09-28T08:27:20Z")
Hi @thermokarst,
thank you for your answer. Great! it worked with that command.
So I first collapse my table at the taxonomic level I am interested, then use "feature-table group" (options: --p-axis sample --m-metadata-file metadata.tsv --m-metadata-column Sampletype --p-mode sum) and then I am able to export the table I wanted.
Now, I tried to create an abundance heatmap from that grouped table in order to have the sample type instead of the samples on one axis. I used the following command:
qiime feature-table heatmap
--i-table table\_collapsed\_bysampletype.qza
--m-metadata-file metadata.tsv
--m-metadata-column Sampletype --p-normalize --p-metric braycurtis
--p-cluster features --o-visualization table\_collapsed\_bysampletype\_heatmap.qzv
It gives me an error saying that "The following IDs are not present in the metadata:" listing the sample types of my metadata. What am I doing wrong?
Thank you very much
Best wishes
Niccolò
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [September 28, 2018, 12:14pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/6 "2018-09-28T12:14:00Z")
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [September 28, 2018, 10:48pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/7 "2018-09-28T22:48:21Z")
Hello @alfanon!
> [@alfanon](#):
>
> What am I doing wrong?
Well, since you have grouped on new values - you have all new Sample IDs, right?
Run `feature-table summarize` on the new table (`table_collapsed_bysampletype.qza`) to see what I mean! 🔍
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [September 28, 2018, 10:48pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/8 "2018-09-28T22:48:23Z")
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### Author:  [@alfanon](https://forum.qiime2.org/u/alfanon)
#### Post date: [October 1, 2018, 3:22pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/9 "2018-10-01T15:22:25Z")
Thank you @thermokarst! I think I have got it. I simply solved it by using the command qiime feature-table heatmap without the –m-metadata-file and –m-metadata-column options.
Sorry to bother you with another question about this topic. I tried to generate a heatmap based on relative frequencies (so I collapsed the table at the level I wanted, then converted to relative frequencies and then used qiime feature-table heatmap). I get the following error:
"Argument to parameter 'table' is not a subtype of FeatureTable[Frequency]"
Is it possible to do what I am trying or the heatmap command already automatically convert itself into relative frequencies?
Thank you
Best
Niccolo
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [October 1, 2018, 3:47pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/10 "2018-10-01T15:47:21Z")
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [October 2, 2018, 3:51am UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/11 "2018-10-02T03:51:51Z")
> [@alfanon](#):
>
> I simply solved it by using the command qiime feature-table heatmap without the –m-metadata-file and –m-metadata-column options.
Perfecto!
> [@alfanon](#):
>
> Sorry to bother you with another question about this topic.
Oh c'mon, no need to apologize - that is what we are here for! ❤ 😃
> [@alfanon](#):
>
> Is it possible to do what I am trying or the heatmap command already automatically convert itself into relative frequencies?
This viz is designed to accept a `FeatureTable[Frequency]` Artifact, not `FeatureTable[RelativeFrequency]`. That is because the action provides its own normalization via the `--p-normalize / --p-no-normalize` parameters:
```bash
--p-normalize / --p-no-normalize
Normalize the feature table by adding a
psuedocount of 1 and then taking the log10
of the table. [default: True]
```
So if I am understanding you correctly, skip the conversion to `FeatureTable[RelativeFrequency]` after you collapse the table and just go straight to the `heatmap`.
:qiime2: 🦖
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [October 2, 2018, 3:51am UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/12 "2018-10-02T03:51:53Z")
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### Author:  [@alfanon](https://forum.qiime2.org/u/alfanon)
#### Post date: [October 3, 2018, 6:53am UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/13 "2018-10-03T06:53:58Z")
Nice from you!
All clear now, thanks a lot 🙂
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [November 3, 2018, 12:54pm UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208/14 "2018-11-03T12:54:02Z")
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