Workflows: panoply_sankey_workflow

panoply_sankey_workflow

Description

PANOPLY workflow to compare sample-membership in a given annotation, between two or more annotation-files. Can optionally take a "primary" annotation file, to be highlighted in the report, and placed in the center of all three-way sankey-diagrams. It is used in the panoply_nmf_workflow workflow compare the results of unsupervised non-negative matrix factorization (NMF)-based clustering, across different clustering-attempts.

The workflow expects an array of sample-annotation file with shared sample-IDs, and a column specifying which annotation-values should be visualized.

The workflow consists of two modules:

module	description
panoply_sankey	create sankey diagram comparison figures
panoply_sankey_report	RMarkown report for panoply_sankey

Input

Required inputs:

• annot_files: (Array[File]+) array of sample-annotation files to be compared (accepts multiple file-format, but prefers .tsv)
• annot_file_labels: (Array[String]+) array of labels uniquely identifying each annotation file (must match length and order of annot_files)
• label: (String) prefix for naming the output tar file

Optional inputs:

• annot_file_primary: (File) sample-annotation file which should be highlighted/centered in diagrams (accepts multiple file-format, but prefers .tsv)

• annot_label_primary: (String) label uniquely identifying the primary annotation file

• id_column: id column for identifying entries (e.g. "Sample.ID"); uses rownames if not provided

• annot_column: annotation column for sankey comparisons (e.g. "NMF.consensus")

• annot_prefix: prefix to prepend to annotation values (e.g. "C" -> C1 C2 C3, instead of 1 2 3)

• color_str: (String) comma-separated string of colors to use for sankey diagrams (e.g. '#AA0000,#0000AA' will assign annotations-subvalues colors on a gradient from red to blue)

Output

• sankey tar - ${label}_sankey_diagrams.tar: Sankey diagrams comparisons between the NMF-clustering-results of supplied -omes.
• sankey report - ${label}_sankey_rmd.html: Summary report of sankey diagram comparisons between the NMF-clustering-results of supplied -omes.