gh-zygi-bio-tool-skills-graphpad-prism/skills/graphpad-prism-skill/reference/script_examples.md

GraphPad Prism Script Examples

Overview

Seven examples demonstrating scripting use cases: repeated imports, Monte Carlo analysis, multi-file consolidation, template workflows, embedded data, multi-table operations, and batch graph formatting.

Example 1: Repeatedly Import Data

Use case: Import multiple data files sequentially into separate tables.

Key commands:

• GoTo D, N - Navigate to data table N
• Import filename.txt - Import external file
• Manual repetition of commands for each file/table

Workflow:

1. Navigate to target table
2. Import file
3. Repeat for each additional file

Limitation: No loop construct in this basic example; requires explicit command repetition.

Example 2: Monte Carlo Analysis

Use case: Perform iterative simulations with randomization.

Key commands:

• ForEach N - Loop N times
• GoTo R, N - Navigate to results table N
• AnalyzeData - Execute analysis
• Next - End loop iteration

Workflow:

1. Set up analysis on initial data
2. Loop through iterations:
   • Generate random data variation
   • Execute analysis
   • Store results in indexed table
3. Aggregate results across iterations

Pattern:

ForEach 100
  GoTo R, %N
  AnalyzeData
  Next

Variable: %N holds current iteration number (1-based).

Example 3: Import Several Files onto One Table

Use case: Consolidate multiple data files into columns of single table.

Key commands:

• GoTo D, 1 - Navigate to data table 1
• Import filename.txt, column=N - Import into specific column N
• Column parameter specifies destination

Workflow:

1. Navigate to target table
2. Import first file to column 1
3. Import subsequent files to columns 2, 3, etc.

Syntax: Import Data1.txt, column=1

Note: Files must have compatible row structure.

Example 4: Open Template and Import Data

Use case: Automate data import into pre-configured analysis template.

Key commands:

• Open template.pzfx - Load template file
• GoTo D, 1 - Navigate to data table
• Import datafile.txt - Import data
• SaveAs output.pzfx - Save populated file

Workflow:

1. Open template with pre-configured graphs/analyses
2. Navigate to data table
3. Import new data
4. Save as new file (preserves template)

Advantage: Template contains all formatting, analysis settings, and graph configurations.

Example 5: Import Data and Info Constants from Script File

Use case: Embed data and metadata directly in script (no external files).

Key commands:

• <DATA>...</DATA> - Data block delimiter
• InsertData N, M - Insert data block N starting at column M
• SetInfo constant_name, value - Set info constant

Data block syntax:

<DATA>
value1\tvalue2\tvalue3
value4\tvalue5\tvalue6
</DATA>

Info constant syntax:

SetInfo Experiment, "Drug Study A"
SetInfo Date, "2024-01-15"
SetInfo Concentration, 10.5

Workflow:

1. Define data blocks in script using <DATA> tags
2. Navigate to target table: GoTo D, 1
3. Insert data: InsertData 1, 0 (block 1, starting column 0)
4. Navigate to info table: GoTo I, 2
5. Set info constants with name/value pairs

Data format: Tab-delimited values within DATA tags, numbered sequentially (1-based).

Info types: String (quoted), numeric (unquoted), date (quoted).

Example 6: Import Data into Several Tables

Use case: Batch import multiple files into multiple tables using loop.

Prerequisites: Prism file with N data tables, each linked to graph, all graphs on one layout.

Key commands:

• ForEach N - Loop N times
• GoTo %N - Navigate to table using iteration variable
• Import Data%N.txt - Dynamic filename with variable substitution
• Next - End loop
• GoTo L, 1 - Navigate to layout
• Print - Print layout

Script pattern:

GoTo D
ForEach 9
  GoTo %N
  Import Data%N.txt
  Next
GoTo L, 1
Print

Variable substitution: %N replaced with current iteration number (1, 2, 3, ..., 9).

Dynamic filenames: Data1.txt, Data2.txt, ..., Data9.txt matched to tables 1-9.

Result: All tables populated, layout printed with all graphs updated.

Example 7: Changing X-Axis Title of All Graphs

Use case: Apply uniform formatting change across all graphs in file.

Key commands:

• GoTo G - Navigate to graphs family
• ForEachSheet - Iterate over all sheets in current family
• SetAxisTitle axis, "title" - Set axis title
• Next - End loop

Script pattern:

GoTo G
ForEachSheet
  SetAxisTitle X, "Time (minutes)"
  Next

Axis parameter: X (X-axis), Y (Y-axis), Y2 (secondary Y-axis).

Scope: Operates on all graph sheets in current family.

Alternative axes: SetAxisTitle Y, "Response (units)" for Y-axis.

Common Scripting Patterns

Loop Constructs

• ForEach N / Next - Fixed iteration count
• ForEachSheet / Next - Iterate over sheets in family
• %N variable - Current iteration number (1-based)

Navigation

• GoTo family, N - Navigate to specific sheet
  • D, N - Data table N
  • R, N - Results table N
  • G, N - Graph N
  • I, N - Info table N
  • L, N - Layout N
• GoTo family - Navigate to family without specific sheet
• GoTo %N - Navigate using iteration variable

Data Operations

• Import filename.txt - Import external file
• Import filename.txt, column=N - Import to specific column
• InsertData N, M - Insert embedded data block N at column M
• <DATA>...</DATA> - Embed data in script (tab-delimited)

Info Constants

• SetInfo name, value - Set named constant
• String values: quoted
• Numeric values: unquoted

File Operations

• Open filename.pzfx - Load Prism file
• SaveAs filename.pzfx - Save with new name

Analysis and Output

• AnalyzeData - Execute analysis
• Print - Print current sheet/layout

Variable Substitution

%N - Current iteration number in loops

• Use in navigation: GoTo %N
• Use in filenames: Import Data%N.txt
• Use in any string context requiring iteration number
• 1-based indexing (first iteration = 1)

Data Formats

External files: Tab-delimited or comma-delimited text files.

Embedded data: Tab-delimited within <DATA> tags, multiple blocks numbered sequentially.

Info constants: Name/value pairs, supports strings (quoted), numbers (unquoted), dates (quoted).

Script Structure Best Practices

1. Navigate before operating: Always GoTo target before import/analysis
2. Use loops for repetitive operations: ForEach with %N variable
3. Embed small datasets: Use <DATA> blocks for portability
4. Template workflows: Separate data from analysis configuration
5. Batch operations: Combine loops with variable substitution for file series
6. Layout printing: Navigate to layout after updating all graphs

Limitations and Notes

• No automatic file discovery: Must specify exact filenames or use predictable naming pattern
• Fixed iteration counts: ForEach N requires known count, no dynamic termination
• Sequential execution: No parallel processing
• Column compatibility: Multi-file imports require matching row structures
• Variable scope: %N only valid within loop construct
• 1-based indexing: All sheet numbers, iteration counts, and data blocks start at 1