Data Analysis Modules: panoply_clumps_ptm_postprocess

panoply_clumps_ptm_postprocess

Description

This module wrangles the results of panoply_clumps_ptm, creating summary figures and visualizations. It creates a dotplot showing the top proteins with clusters of differentially-upregulated, and differentially down-regulated PTM-sites, for each annotation value tested. It also creates PyMol figures for the top significant proteins, with the location of modified residues colored.

Input

Required inputs:

• results_tar: (.tar file) tar file containing the results of panoply_clumps_ptm
• output_prefix: (String, default="results") prefix used to name the output files
• yaml_file: (.yaml file) master-parameters.yaml

Optional inputs:

• fdr_threshold: (Float) FDR threshold for significance
• pymol_gen: (Boolean, default=true) if TRUE, PyMol figures will be generated
• pymol_upper_limit: (Int, default=10) maximum number of PyMol figures that should be generated per test

Output

• results: ("${output_prefix}_clumps_ptm_full_results.tar") all results and figures of ClumpsPTM, including data-tables and raw results
• figures_only: ("${output_prefix}_clumps_figures.tar") summary figures and PyMol only