cluster_jaccard: Perform Jaccard clustering of pathways and output results to...

In ayushnoori/brainstorm: Personal Utility Functions

Perform Jaccard clustering of pathways and output results to an Excel workbook.

Description

This function performs hierarchical clustering on gene sets (pathways) based on the Jaccard similarity of their gene members. It subsets pathways from the supplied pathway_table using the specified contrast, computes the similarity matrix, performs hierarchical clustering, and generates a dendrogram saved as a PDF. The function then annotates the pathways with cluster information (using annotate_clusters()) and writes the result to a specified worksheet in an openxlsx workbook via add_table_to_workbook().

Usage

cluster_jaccard(contrast, contrast_color, wb, pathway_table)

Arguments

contrast	A character string specifying the contrast (e.g., "WT vs. GFP") used to subset the pathways.
contrast_color	A character string representing the tab color (as a hex code, e.g., "#FAE1DD") for the worksheet corresponding to this contrast.
wb	A workbook object created by openxlsx::createWorkbook() where the clustered results will be added.
pathway_table	A data.table containing the pathways to be clustered. This table must include the following columns: Contrast, MEMBERS_SYMBOLIZED, NAME, Comparison, Regulation, SIZE, ES, NES, NOM.p.val, FDR.q.val, FWER.p.val, CONTRIBUTOR, SUB_CATEGORY_CODE, EXACT_SOURCE, DESCRIPTION_BRIEF, and MEMBERS_EZID.

Details

The dendrogram is saved as a PDF in the "Results/GSEA_preranked/pathways" directory relative to the project root.

Value

A data.table containing the pathways annotated with cluster information.

See Also

compute_jaccard_similarity, annotate_clusters, add_table_to_workbook

ayushnoori/brainstorm documentation built on April 14, 2025, 4:12 p.m.