# How to run multiple metrics, methods options in qiime2 feature table heatmap

**URL:** https://forum.qiime2.org/t/how-to-run-multiple-metrics-methods-options-in-qiime2-feature-table-heatmap/6878
**Category:** User Support
**Created:** [November 9, 2018, 3:51pm UTC](https://forum.qiime2.org/t/how-to-run-multiple-metrics-methods-options-in-qiime2-feature-table-heatmap/6878 "2018-11-09T15:51:31Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![Prasad\_Gajare](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/p/46a35a/32.png) [@Prasad\_Gajare](https://forum.qiime2.org/u/Prasad_Gajare)
#### Post date: [November 9, 2018, 3:51pm UTC](https://forum.qiime2.org/t/how-to-run-multiple-metrics-methods-options-in-qiime2-feature-table-heatmap/6878/1 "2018-11-09T15:51:31Z")

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Hello,

I am trying to generate various heatmaps using different metric(--p-metric) and methods(--p-method).  
By using following command:

qiime feature-table heatmap --i-table feature-table.qza --m-metadata-file meta\_data.txt --m-metadata-column Syndrome\_V2 --p-metric braycurtis --p-method weighted --p-color-scheme rainbow --p-cluster features --o-visualization braycurtis\_weighted\_heatmap\_filtered\_clusted.qzv

Is there are by which I can run all different metrics and methods in just command line.  
I tried using "," and "|" to input different metric in above command but it gives error saying invalid value.

Please see the command I used below.

qiime feature-table heatmap --i-table feature-table.qza --m-metadata-file meta\_data.txt --m-metadata-column Syndrome\_V2 --p-metric **braycurtis, canberra** --p-method weighted --p-color-scheme rainbow --output-dir test

Usage: qiime feature-table heatmap [OPTIONS]

Error: Invalid value for "--p-metric": invalid choice: braycurtis,. (choose from canberra, correlation, sokalsneath, sqeuclidean, cityblock, mahalanobis, sokalmichener, rogerstanimoto, dice, minkowski, russellrao, chebyshev, euclidean, yule, hamming, cosine, jaccard, seuclidean, braycurtis, kulsinski, matching)

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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [November 9, 2018, 3:53pm UTC](https://forum.qiime2.org/t/how-to-run-multiple-metrics-methods-options-in-qiime2-feature-table-heatmap/6878/2 "2018-11-09T15:53:26Z")

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> [@Prasad\_Gajare](#):
>
> Is there are by which I can run all different metrics and methods in just command line.

That QIIME 2 command does not support multiple metrics simultaneously. You can write a bash loop to generate multiple heatmaps.

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### Author: ![Prasad\_Gajare](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/p/46a35a/32.png) [@Prasad\_Gajare](https://forum.qiime2.org/u/Prasad_Gajare)
#### Post date: [November 9, 2018, 4:38pm UTC](https://forum.qiime2.org/t/how-to-run-multiple-metrics-methods-options-in-qiime2-feature-table-heatmap/6878/3 "2018-11-09T16:38:12Z")

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Thanks for replying quickly.

Yeah I just wanted to make sure if there was an option to do without writing bash loop.

Thanks again

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [December 10, 2018, 10:40pm UTC](https://forum.qiime2.org/t/how-to-run-multiple-metrics-methods-options-in-qiime2-feature-table-heatmap/6878/4 "2018-12-10T22:40:42Z")

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