Generate Workflow Diagram

Make themed Mermaid flowchart diagram from putior workflow data. Embed in docs.

When Use

• After annotating source files, ready to make visual diagram
• Regenerate diagram after workflow changes
• Switch themes or output formats for different audiences
• Embed workflow diagrams in README, Quarto, R Markdown docs

Inputs

• Required: Workflow data from put(), put_auto(), or put_merge()
• Optional: Theme name (default: "light"; options: light, dark, auto, minimal, github, viridis, magma, plasma, cividis)
• Optional: Output target: console, file path, clipboard, raw string
• Optional: Interactive features: show_source_info, enable_clicks

Steps

Step 1: Extract Workflow Data

Get workflow data from one of three sources.

library(putior)

# From manual annotations
workflow <- put("./src/")

# From manual annotations, excluding specific files
workflow <- put("./src/", exclude = c("build-workflow\\.R$", "test_"))

# From auto-detection only
workflow <- put_auto("./src/")

# From merged (manual + auto)
workflow <- put_merge("./src/", merge_strategy = "supplement")

Workflow data frame may include node_type column from annotations. Node types control Mermaid shapes:

node_type	Mermaid Shape	Use Case
"input"	Stadium ([...])	Data sources, configuration files
"output"	Subroutine [[...]]	Generated artifacts, reports
"process"	Rectangle [...]	Processing steps (default)
"decision"	Diamond {...}	Conditional logic, branching
"start" / "end"	Stadium ([...])	Entry/terminal nodes

Each node_type also gets CSS class (class nodeId input;) for theme-based styling.

Got: Data frame with at least one row, has id, label, optionally input, output, source_file, node_type columns.

If fail: Data frame empty? No annotations or patterns found. Run analyze-codebase-workflow first, or check annotations syntactically valid with put("./src/", validate = TRUE).

Step 2: Pick Theme + Options

Pick theme for target audience.

# List all available themes
get_diagram_themes()

# Standard themes
# "light"   — Default, bright colors
# "dark"    — For dark mode environments
# "auto"    — GitHub-adaptive with solid colors
# "minimal" — Grayscale, print-friendly
# "github"  — Optimized for GitHub README files

# Colorblind-safe themes (viridis family)
# "viridis" — Purple→Blue→Green→Yellow, general accessibility
# "magma"   — Purple→Red→Yellow, high contrast for print
# "plasma"  — Purple→Pink→Orange→Yellow, presentations
# "cividis" — Blue→Gray→Yellow, maximum accessibility (no red-green)

Additional parameters:

• direction: Diagram flow direction — "TD" (top-down, default), "LR" (left-right), "RL", "BT"
• show_artifacts: TRUE/FALSE — show artifact nodes (files, data); noisy for large workflows (16+ extra nodes)
• show_workflow_boundaries: TRUE/FALSE — wrap each source file nodes in Mermaid subgraph
• source_info_style: How source file info displayed on nodes (subtitle)
• node_labels: Format for node label text

Got: Theme names printed. Pick one by context.

If fail: Theme name not recognized? put_diagram() falls back to "light". Check spelling.

Step 3: Custom Palette with put_theme() (Optional)

9 built-in themes don't match project palette? Make custom theme with put_theme().

# Create custom palette — unspecified types inherit from base theme
cyberpunk <- put_theme(
  base = "dark",
  input    = c(fill = "#1a1a2e", stroke = "#00ff88", color = "#00ff88"),
  process  = c(fill = "#16213e", stroke = "#44ddff", color = "#44ddff"),
  output   = c(fill = "#0f3460", stroke = "#ff3366", color = "#ff3366"),
  decision = c(fill = "#1a1a2e", stroke = "#ffaa33", color = "#ffaa33")
)

# Use the palette parameter (overrides theme when provided)
mermaid_content <- put_diagram(workflow, palette = cyberpunk, output = "raw")
writeLines(mermaid_content, "workflow.mmd")

put_theme() takes input, process, output, decision, artifact, start, end node types. Each takes named vector c(fill = "#hex", stroke = "#hex", color = "#hex"). Unset types inherit from base theme.

Got: Mermaid output with custom classDef lines. Node shapes from node_type preserved; only colors change. All node types use stroke-width:2px — override not supported via put_theme().

If fail: Palette object not putior_theme class? put_diagram() raises descriptive error. Pass return value of put_theme(), not raw list.

Fallback — manual classDef replacement: Fine-grained control beyond put_theme() (per-type stroke widths)? Generate with base theme + replace classDef lines manually:

mermaid_content <- put_diagram(workflow, theme = "dark", output = "raw")
lines <- strsplit(mermaid_content, "\n")[[1]]
lines <- lines[!grepl("^\\s*classDef ", lines)]
custom_defs <- c("  classDef input fill:#1a1a2e,stroke:#00ff88,stroke-width:3px,color:#00ff88")
mermaid_content <- paste(c(lines, custom_defs), collapse = "\n")

Step 4: Generate Mermaid Output

Make diagram in desired output mode.

# Print to console (default)
cat(put_diagram(workflow, theme = "github"))

# Save to file
writeLines(put_diagram(workflow, theme = "github"), "docs/workflow.md")

# Get raw string for embedding
mermaid_code <- put_diagram(workflow, output = "raw", theme = "github")

# With source file info (shows which file each node comes from)
cat(put_diagram(workflow, theme = "github", show_source_info = TRUE))

# With clickable nodes (for VS Code, RStudio, or file:// protocol)
cat(put_diagram(workflow,
  theme = "github",
  enable_clicks = TRUE,
  click_protocol = "vscode"  # or "rstudio", "file"
))

# Full-featured
cat(put_diagram(workflow,
  theme = "viridis",
  show_source_info = TRUE,
  enable_clicks = TRUE,
  click_protocol = "vscode"
))

Got: Valid Mermaid code starts with flowchart TD (or LR by direction). Nodes connected by arrows showing data flow.

If fail: Output is flowchart TD with no nodes? Workflow data frame empty. Connections missing? Check output filenames match input filenames across nodes.

Step 5: Embed in Target Document

Insert diagram into appropriate docs format.

GitHub README (```mermaid code fence):

## Workflow

```mermaid
flowchart TD
  A["Extract Data"] --> B["Transform"]
  B --> C["Load"]
```

Quarto document (native mermaid chunk via knit_child):

# Chunk 1: Generate code (visible, foldable)
workflow <- put("./src/")
mermaid_code <- put_diagram(workflow, output = "raw", theme = "github")

# Chunk 2: Output as native mermaid chunk (hidden)
#| output: asis
#| echo: false
mermaid_chunk <- paste0("```{mermaid}\n", mermaid_code, "\n```")
cat(knitr::knit_child(text = mermaid_chunk, quiet = TRUE))

R Markdown (with mermaid.js CDN or DiagrammeR):

DiagrammeR::mermaid(put_diagram(workflow, output = "raw"))

Got: Diagram renders correct in target format. GitHub renders mermaid code fences native.

If fail: GitHub won't render diagram? Code fence must use exactly ```mermaid (no extra attributes). Quarto → use knit_child() approach since direct variable interpolation in {mermaid} chunks not supported.

Checks

• put_diagram() produces valid Mermaid code (starts with flowchart)
• All expected nodes appear in diagram
• Data flow connections (arrows) present between connected nodes
• Selected theme applied (check init block in output for theme-specific colors)
• Diagram renders correct in target format (GitHub, Quarto)

Pitfalls

• Empty diagrams: Usually put() returned no rows. Check annotations exist + syntactically valid.
• All nodes disconnected: Output filenames must exactly match input filenames (including extension) for putior to draw connections. data.csv + Data.csv are different.
• Theme not visible on GitHub: GitHub mermaid renderer has limited theme support. "github" theme designed for GitHub. %%{init:...}%% theme block may be ignored by some renderers.
• Quarto mermaid variable interpolation: Quarto {mermaid} chunks don't support R variables direct. Use knit_child() from Step 5.
• Clickable nodes not working: Click directives need renderer supporting Mermaid interaction events. GitHub static renderer no click support. Use local Mermaid renderer or putior Shiny sandbox.
• Self-referential meta-pipeline files: Scanning directory including build script generating diagram → duplicate subgraph IDs + Mermaid errors. Use exclude parameter:

  workflow <- put("./src/", exclude = c("build-workflow\\.R$", "build-workflow\\.js$"))
  

• show_artifacts = TRUE too noisy: Large projects generate many artifact nodes (10–20+), clutter diagram. Use show_artifacts = FALSE + rely on node_type annotations to mark key inputs/outputs explicit.

See Also

• annotate-source-files — prerequisite: files annotated before diagram generation
• analyze-codebase-workflow — auto-detection supplements manual annotations
• setup-putior-ci — automate diagram regeneration in CI/CD
• create-quarto-report — embed diagrams in Quarto reports
• build-pkgdown-site — embed diagrams in pkgdown docs sites