Option that allows you to run qiime emperor plots on multiple pcoa_results.qza artifacts in a single command

Ideas and Suggestions
,
1

It can be a bit tedious having to run multiple commands when making output visualizations for the 3 pcoa_results.qza artifacts outputted from the qiime diversity core-metrics command (e.g.,

qiime emperor plot \
  --i-pcoa cm1441/unweighted_unifrac_pcoa_results.qza \
  --m-metadata-file sample-metadata.tsv \
  --p-custom-axis DaysSinceExperimentStart \
  --o-visualization cm1441/unweighted-unifrac-emperor.qzv

qiime emperor plot \
  --i-pcoa cm1441/weighted_unifrac_pcoa_results.qza \
  --m-metadata-file sample-metadata.tsv \
  --p-custom-axis DaysSinceExperimentStart \
  --o-visualization cm1441/weighted-unifrac-emperor.qzv

qiime emperor plot \
  --i-pcoa cm1441/bray_curtis_pcoa_results.qza \
  --m-metadata-file sample-metadata.tsv \
  --p-custom-axis DaysSinceExperimentStart \
  --o-visualization cm1441/bray-curtis-emperor.qzv

Could an option be added that would make it so you only have to run the command once and you can get a visual output on whichever and however many pcoa_results.qza artifacts you want? This could also be applied to other output visualizations like (alpha-group-significance ,beta-group-significance, alpha-group-significance ect…).

My current work around is:

cd core_metrics_output

for file in *pcoa_results.qza; 
do 
echo "Running qiime emperor plot"
qiime emperor plot --i-pcoa $file --m-metadata-file filtered_mapping_file.tsv --o-visualization ${file%}-emperor.qzv
done
3 Likes
3

Hi @pjtorres! We are planning on supporting pipelines in the future, which will have the ability to output artifacts (.qza) and/or visualizations (.qzv). These QIIME 2 “pipelines” will be similar in nature to QIIME 1 “workflows” with additional functionality. When pipelines are supported, the core-metrics method will be converted into a pipeline and Emperor visualizations will be included in its output.

Thanks for getting in touch!

3 Likes
5

Pipelines are now supported in the latest QIIME 2 release (2017.10)! core-metrics and core-metrics-phylogenetic now output Emperor plots for each beta diversity metric. :tada:

1 Like