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


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)

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

1 Like

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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