putior (version 0.1.0)

put_diagram: Create Mermaid Diagram from PUT Workflow

Description

Generates a Mermaid flowchart diagram from putior workflow data, showing the flow of data through your analysis pipeline.

Usage

put_diagram(
  workflow,
  output = "console",
  file = "workflow_diagram.md",
  title = NULL,
  direction = "TD",
  node_labels = "label",
  show_files = FALSE,
  show_artifacts = FALSE,
  show_workflow_boundaries = TRUE,
  style_nodes = TRUE,
  theme = "light"
)

Value

Character string containing the mermaid diagram code

Arguments

workflow

Data frame returned by put() containing workflow nodes

output

Character string specifying output format. Options:

• "console" - Print to console (default)

• "file" - Save to file specified by file parameter

• "clipboard" - Copy to clipboard (if available)

• "raw" - Return raw mermaid code without markdown fences (for knitr/pkgdown)

file

Character string specifying output file path (used when output = "file")

title

Character string for diagram title (optional)

direction

Character string specifying diagram direction. Options: "TD" (top-down), "LR" (left-right), "BT" (bottom-top), "RL" (right-left)

node_labels

Character string specifying what to show in nodes: "name" (node IDs), "label" (descriptions), "both" (ID: label)

show_files

Logical indicating whether to show file connections

show_artifacts

Logical indicating whether to show data files as nodes. When TRUE, creates nodes for all input/output files, not just script connections. This provides a complete view of the data flow including terminal outputs.

show_workflow_boundaries

Logical indicating whether to apply special styling to nodes with node_type "start" and "end". When TRUE, these nodes get distinctive workflow boundary styling (icons, colors). When FALSE, they render as regular nodes.

style_nodes

Logical indicating whether to apply styling based on node_type

theme

Character string specifying color theme. Options: "light" (default), "dark", "auto" (GitHub adaptive), "minimal", "github"

Examples

if (FALSE) {
# Basic usage - shows only script connections
workflow <- put("./src/")
put_diagram(workflow)

# Show all data artifacts as nodes (complete data flow)
put_diagram(workflow, show_artifacts = TRUE)

# Show artifacts with file labels on connections
put_diagram(workflow, show_artifacts = TRUE, show_files = TRUE)

# Show workflow boundaries with special start/end styling
put_diagram(workflow, show_workflow_boundaries = TRUE)

# Disable workflow boundaries (start/end nodes render as regular)
put_diagram(workflow, show_workflow_boundaries = FALSE)

# GitHub-optimized theme for README files
put_diagram(workflow, theme = "github")

# Save to file with artifacts enabled
put_diagram(workflow, show_artifacts = TRUE, output = "file", file = "workflow.md")

# For use in knitr/pkgdown - returns raw mermaid code
# Use within a code chunk with results='asis'
cat("```mermaid\n", put_diagram(workflow, output = "raw"), "\n```\n")
}