Sample Group Sankey Plot

Sample Group Sankey Plot

Builds a reproducible Sankey/alluvial visualization from a tabular sample annotation file and exports the selected annotations, lodes-format table, plot PDF, and session metadata.

Input Validation

This skill accepts: a sample annotation table in CSV or TSV format where rows are samples and selected columns are categorical stages (e.g., risk group, response status, subtype, cohort label). At least 2 stage columns are required.

If the user's request does not involve generating a Sankey or alluvial flow diagram from categorical sample annotations — for example, asking to visualize a gene regulatory network, plot continuous-value trajectories, analyze pathway flow, or process non-tabular data — do not proceed with the workflow. Instead respond:

"sample-group-sankey-plot is designed to generate Sankey/alluvial plots from categorical sample annotation tables. Your request appears to be outside this scope. Please provide a sample annotation table with at least 2 categorical stage columns, or use a more appropriate tool for gene network visualization or pathway analysis."

Readability guidance: Sankey plots are recommended for fewer than 8 unique values per stage and fewer than 5 stages total. For larger inputs, filter or aggregate categories before plotting to ensure readable output.

Agent Response Contract

After a successful run, report to the caller:

Copy code
Sankey plot generated successfully.
Stages plotted : <comma-separated stage column names>
Samples        : <row count>
Output prefix  : <output_prefix>
Outputs:
  table/selected_annotations.csv
  table/sankey_lodes.csv
  plot/<output_prefix>.pdf
  data/session_info.txt
Readability warnings (if any): <advisory messages or "none">

If the script exits with a non-zero status, surface the SKILL_* error code and message verbatim. Do not attempt to continue or retry silently.

When to Read External Files

→ Reference files algorithm.md, troubleshooting.md, and cli-guide.md are in references/. If absent, rely on the Error Handling table below for common issues.

Usage

Environment Setup

Install required R packages before the first run:

bashCopy code
Rscript scripts/install_dependencies.R

Note: install_dependencies.R installs from CRAN without version pinning. Tested with ggalluvial >= 0.12.5 and ggplot2 >= 3.4.0. For reproducible CI environments, consider using remotes::install_version().

Basic Command

bashCopy code
Rscript scripts/main.R \
  --input_file ./annotations.csv \
  --output_dir ./output \
  --columns risk,Responder \
  --seed 42

Arguments

Input Format

Annotation Table (input_file)

Delimited text file where rows represent samples and each selected column is a categorical stage shown in the Sankey plot.

csvCopy code
SampleID,risk,Responder,Subtype
S1,High,Yes,Basal
S2,Low,No,LumA
S3,High,Yes,Basal
S4,Low,No,LumB

Requirements:

• The file must contain at least 2 columns if --columns is omitted.
• Each selected column must exist in the file header.
• Selected columns are interpreted as categorical stages and will be converted to character values.
• Blank strings and NA values are replaced with --missing_label.
• CSV and TSV inputs are supported.
• Recommended: fewer than 8 unique values per stage and fewer than 5 stages total for readable plots.

Output Files

selected_annotations.csv

sankey_lodes.csv

Workflow

Step 1: Validate Input

• Check that the input file exists and is readable.
• Detect CSV vs TSV input.
• Validate that at least 2 stage columns are available.
• Validate that user-specified columns exist.

Step 2: Prepare Sankey Data

• Subset the selected stage columns.
• Replace missing or blank labels.
• Add a row-level sample_id identifier.
• Convert the table with ggalluvial::to_lodes_form().

Step 2a: Readability Advisories

After column selection, the script emits log_warn advisories when:

• More than 5 stages are selected: "More than 5 stages selected; plot may be hard to read. Consider filtering."
• A stage has more than 8 unique values: "Stage <name> has <n> unique values; consider aggregating for readability."

These are advisory only — the script continues and produces the plot.

Step 3: Generate Visualization

• Build the Sankey/alluvial plot with geom_flow() and geom_stratum().
• Render stratum labels.
• Save the plot as PDF.

Step 4: Record Outputs

• Save the selected annotations and lodes-format table as CSV files.
• Save sessionInfo() and runtime arguments for reproducibility.

Examples

Reproduce the Original Two-Column Plot

bashCopy code
Rscript scripts/main.R \
  -i tests/data/sample_annotations.csv \
  -o tests/output \
  -c risk,Responder

Plot Three Annotation Stages

bashCopy code
Rscript scripts/main.R \
  -i tests/data/sample_annotations.csv \
  -o tests/output_three_stage \
  -c risk,Responder,Subtype \
  --title "Risk to response transitions"

Use All Columns Automatically

bashCopy code
Rscript scripts/main.R \
  -i tests/data/minimal_annotations.csv \
  -o tests/output_all_columns

Error Handling

Common Errors

IF error persists, READ: references/troubleshooting.md

Testing

Test with Sample Data

bashCopy code
Rscript scripts/install_dependencies.R

Rscript scripts/main.R --help

Rscript scripts/main.R \
  -i tests/data/sample_annotations.csv \
  -o tests/output \
  -c risk,Responder,Subtype

Rscript tests/test_skill.R

Rscript tests/run_smoke_test.R

Validation Commands

bashCopy code
ls -la tests/output/table
ls -la tests/output/plot
ls -la tests/output/data

References

1. Brunson JC (2020) ggalluvial: Layered Grammar for Alluvial Plots. Journal of Open Source Software. doi:10.21105/joss.02017
2. Wickham H (2016) ggplot2: Elegant Graphics for Data Analysis. Springer. doi:10.1007/978-3-319-24277-4

For detailed algorithm, READ: references/algorithm.md