Report Modules: panoply_association_report

panoply_association_report

Description

This module creates an interactive R Markdown report of the GSEA results of the panoply_association module. For each contrast, an interactive volcano plot shows the Normalized Enrichment Score (NES) vs -log10 of the FDR value for each database pathway analyzed. Hovering over a point reveals which pathway it corresponds to. Any significantly enriched pathways (determined by the fdr_value input) are highlighted in red and described in an interactive, searchable table. For multi-contrast categories, an overview heatmap shows NES values for all contrasts, with asterisks denoting signficant enrichment.

Input

Required inputs:

• ssgsea_assoc_tars: (.tar file) output tar file(s) containing results from panoply_association
• master_yaml: (.yaml file) master parameters file
• label: (String) directory name within the tar file
• type: (String) data (-ome) type

Optional inputs:

• fdr_value: (Float, default = 0.01) FDR value cutoff to be considered significant.

Output

• report_out: (.html file) Interactive R Markown report.