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Create Mermaid Diagram from PUT Workflow

Source: R/put_diagram.R
put_diagram.Rd

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",
  palette = NULL,
  show_source_info = FALSE,
  source_info_style = "inline",
  enable_clicks = FALSE,
  click_protocol = "vscode",
  log_level = NULL
)

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 light theme with bright colors (default)

  • "dark" - Dark theme for dark mode environments

  • "auto" - GitHub-adaptive with solid colors for both modes

  • "minimal" - Grayscale professional, print-friendly

  • "github" - Optimized for GitHub README files

  • "viridis" - Colorblind-safe (purple-blue-green-yellow)

  • "magma" - Colorblind-safe warm (purple-red-yellow)

  • "plasma" - Colorblind-safe vibrant (purple-pink-yellow)

  • "cividis" - Colorblind-safe for deuteranopia/protanopia (blue-yellow)

The viridis family themes are perceptually uniform and tested for accessibility.

palette

Optional putior_theme object created by put_theme() for custom node colors. When provided, this overrides the theme parameter. Default is NULL (use theme).

show_source_info

Logical indicating whether to display source file information in diagram nodes. When TRUE, each node shows its originating file name. Default is FALSE for backward compatibility.

source_info_style

Character string specifying how to display source info:

  • "inline" - Append file name to node labels (default)

  • "subgraph" - Group nodes by source file into Mermaid subgraphs

enable_clicks

Logical indicating whether to add click directives to nodes. When TRUE, nodes become clickable links that open the source file in an editor. Default is FALSE for backward compatibility.

click_protocol

Character string specifying the URL protocol for clickable nodes:

  • "vscode" - VS Code editor (vscode://file/path:line) (default)

  • "file" - Standard file:// protocol

  • "rstudio" - RStudio IDE (rstudio://open-file?path=)

log_level

Character string specifying log verbosity for this call. Overrides the global option putior.log_level when specified. Options: "DEBUG", "INFO", "WARN", "ERROR". See set_putior_log_level.

Value

Character string containing the mermaid diagram code

Examples

if (FALSE) { # \dontrun{
# 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")

# Show source file info inline in nodes
put_diagram(workflow, show_source_info = TRUE)

# Group nodes by source file using subgraphs
put_diagram(workflow, show_source_info = TRUE, source_info_style = "subgraph")

# Enable clickable nodes (opens in VS Code)
put_diagram(workflow, enable_clicks = TRUE)

# Enable clickable nodes with RStudio protocol
put_diagram(workflow, enable_clicks = TRUE, click_protocol = "rstudio")

# Use a custom color palette
my_theme <- put_theme(base = "dark",
  input = c(fill = "#1a5276", stroke = "#2e86c1", color = "#ffffff"))
put_diagram(workflow, palette = my_theme)
} # }