Prepare Pathway Scores for Heatmap Visualization

This function prepares a tidy table of pathway scores joined with sample annotations from a `SummarizedExperiment` object. It returns a list suitable for heatmap plotting.

Usage

prep_scores_hm(exp_data, pathway_scores, pathways = 1:20)

Arguments

exp_data

A `SummarizedExperiment` object containing sample annotations in `colData`.

pathway_scores

A matrix or data frame with pathway scores (rows = pathways, columns = samples).

pathways

Either a numeric vector indicating indices of pathways to include, or a character vector of pathway names. Default is 1:20.

Value

A list containing:

table

A data frame in wide format with pathway scores and sample metadata.

colv

Column to use as identifier for samples (usually `"sample_id"`).

rowv

A character vector of selected pathways.