TSV/Dir Pipeline Information

This is information regarding q2-ps-plot’s and q2-autopepsirf’s TSV/Dir pipelines, as well as tutorials on how to use the various tsv/dir pipelines.

Available TSV/Dir pipelines

q2-ps-plot:

QZA Modules

Corresponding TSV/Dir Pipeline

mutant_scatter

Coming Soon!

proteinHeatmap

proteinHeatmap-dir

repScatters

repScatters-tsv

zenrich

zenrich-tsv

q2-autopepsirf:

QZA Modules

Corresponding TSV/Dir Pipeline

diffEnrich

diffEnrich-tsv

TSV/Dir Pipeline Tutorials

Instead of inputting a QZA file in an input (–i-flag), a TSV file or directory filepath is inputted into a different parameters flag typically ending in “-filepath” (–p-flag-filepath).

proteinHeatmap:

  • QZA Module Example:

    qiime ps-plot proteinHeatmap --i-enriched-dir enriched-dir.qza --i-protein-alignment alignment.qza --o-visualization proteinHeatmap.qzv

  • TSV/Dir Pipeline Example:

    qiime ps-plot proteinHeatmap-dir --p-enriched-dir-filepath enriched-dir/ --p-protein-alignment-filepath alignment/ --o-protein-heatmap-vis proteinHeatmap.qzv

repScatters:

  • QZA Module Example:

    qiime ps-plot repScatters --i-zscore some-zscore.qza --m-source-file samples-source.tsv --m-source-column source --o-visualizaion repScatters.qza

  • TSV/Dir Pipeline Example:

    qiime ps-plot repScatters-tsv --p-zscore-filepath some-zscore.tsv --m-source-file samples-source.tsv --m-source-column source --o-rep-scatters-vis repScatters.qzv

zenrich:

  • QZA Module Example:

    qiime ps-plot zenrich --i-data col-sum.qza --i-zscores zscores.qza --p-negative-id someID --m-source-file samples-source.tsv --m-soure-column source --p-exact-cs-thresh 0 --p-pepsirf-binary pepsirf --o-visualization zenrich.qzv

  • TSV/Dir Pipeline Example:

    qiime ps-plot zenrich-tsv --p-data-filepath col-sum.tsv --p-zscores-filepath zscores.tsv --p-negative-id someID --m-source-file samples-source.tsv --m-soure-column source --p-exact-cs-thresh 0 --p-pepsirf-binary pepsirf --o-zenrich-vis zenrich.qzv

diffEnrich:

  • QZA Module Example:

    qiime autopepsirf diffEnrich --i-raw-data raw-data.qza --i-bins bins.qza --p-negative-id someID --p-exact-z-thresh 6,10 --p-pepsirf-tsv-dir testingTSV/ --p-tsv-base-str baseString --p-hdi 0.95 --p-pepsirf-binary pepsirf --output-dir autopepsirf-diffEnrich

  • TSV/Dir Pipeline Example:

    qiime autopepsirf diffEnrich-tsv --p-raw-data-filepath raw-data.tsv --p-bins-filepath bins.tsv --p-negative-id someID --p-exact-z-thresh 6,10 --p-pepsirf-tsv-dir testingTSV/ --p-tsv-base-str baseString --p-hdi 0.95 --p-pepsirf-binary pepsirf --output-dir autopepsirf-diffEnrich