Summarize and Visualize Analysis Pipeline Steps — run_pipeline

This function prints and visualizes the analysis steps stored in the metadata of a MultiAssayExperiment object. The steps are optionally printed to the console as a numbered list and can be rendered as a left-to-right Mermaid flowchart. The flowchart connects steps with arrows and includes step notes if requested.

Usage

run_pipeline_summary(
  expomicset,
  show_index = TRUE,
  console_print = TRUE,
  diagram_print = FALSE,
  include_notes = TRUE
)

Arguments

expomicset: A MultiAssayExperiment object that contains a "summary" entry in its metadata, which includes a list named steps.
show_index: Logical, default TRUE. If TRUE, prefixes each step with its index.
console_print: Logical, default TRUE. If TRUE, prints the step list to the console.
diagram_print: Logical, default FALSE. If TRUE, renders a Mermaid diagram of the steps.
include_notes: Logical, default TRUE. If TRUE, appends any "notes" associated with each step to the label.

Value

No return value. This function is called for its side effects: console output and/or diagram rendering.

Details

The Mermaid flowchart is rendered left-to-right and connects each step in sequence. Each node is labeled using the step name and, optionally, any attached notes.

Examples

if (FALSE) { # \dontrun{
run_pipeline_summary(expomicset)
} # }