Report Modules: panoply_sampleqc_report

panoply_sampleqc_report

Description

This module creates an interactive R Markdown report for the panoply_sampleqc module.

The report provides:

• Interactive box-whisker plots visualizing the distributions of stromal, immune and tumor purity scores inferred by ESTIMATE across data types.

• Interactive heatmaps visualizing pairwise sample correlations between RNA, CNA and proteome data to expore potential sample swaps. Heatmaps are created with the MORPHEUS R-package.

Input

Required inputs:

• tarball: (.tar file) tarball from panoply_sampleqc
• label: (String) label
• type: (String) data (-ome) type
• tmpDir: (String, default="tmp") name of directory used to extract the tarball

Output

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