Report Modules: panoply_nmf_report

panoply_nmf_report

Description

This module creates an R markdown report for the panoply_nmf module. The report provides:

• Table summarizing the number of features per data type used in the clustering.

• Interactive line graph illustrating different cluster metrics as a function of the number of clusters tested. The optimal number of clusters is indicated as vertical line.

• Table summarizing the number of samples in each cluster.

• Heatmap depicting the relative contributions of each sample to each cluster.

• Table summarizing the results of an overrepresentation analysis of sample metadata terms (e.g. clinical annotation, inferred phenotypes, etc.) in each cluster.

• Heatmap depicting the abundances of cluster specific features across clusters.

• Barpchart depicting the number of cluster specific features.

• Browsable table of all cluster-specific features.

• Heatmap depicting the consensus matrix across multiple random restarts of NMF.

• Silhouette plot depicting cluster stability.

• Table listing all parameters used in panoply_nmf and panoply_nmf_postprocess.

Input

Required inputs:

• nmf_results: (.tar file) tarball from panoply_nmf
• postprocess_tarball: (.tar file) tarball from panoply_nmf_postprocess
• nclust: (Int) Factorization rank used in panoply_nmf_postprocess
• label: (String) label used in the report title

Output

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