Function help added #55
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Pull Request Overview
This PR adds comprehensive function documentation for two main files in the package, with detailed descriptions, parameter explanations, and examples. The documentation follows modern R documentation standards with @importFrom directives and proper formatting.
- Adds detailed function documentation with descriptions, parameters, return values, and examples
- Includes proper @importFrom statements for package dependencies
- Adds executable code examples (some wrapped in \dontrun{} for safety)
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
| R/functions_degs.R | Comprehensive documentation for differential expression analysis functions, ORA/GSEA functions, and utility functions |
| R/functions_analysis.R | Complete documentation for matrix operations, normalization, dimensionality reduction, and integration functions |
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| #' deg_result <- DegsRunTest(contrast) | ||
| #' DegsScatterPlot(deg_result, n_label = 10, font_size = 12) | ||
| #' } | ||
| DegsScatterPlot = function(deg_result, n_label=5, font_size=11) { |
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The function signature has changed to include a new parameter n_label but the function body still references hardcoded values for top DEGs (line 2072). The parameter should be used consistently throughout the function implementation.
| #' deg_result <- DegsRunTest(contrast) | ||
| #' DegsVolcanoPlot(deg_result, n_label = 10, font_size = 12) | ||
| #' } | ||
| DegsVolcanoPlot = function(deg_result, n_label=5, font_size=11) { |
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Similar to DegsScatterPlot, the function signature includes n_label parameter but the function body may still use hardcoded values. Ensure the parameter is properly utilized in the implementation.
| valid_feature_selection_methods = c("vst", "scran") | ||
| assertthat::assert_that(feature_selection_method %in% valid_feature_selection_methods, | ||
| msg=FormatString("Variable features method must must be one of: {valid_feature_selection_methods*}.")) | ||
| msg=FormatString("Variable features method must be one of: {valid_feature_selection_methods*}.")) |
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There is a duplicated word 'must' in the error message. It should read 'Variable features method must be one of:' instead of 'must must be'.
R/functions_degs.R
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| } | ||
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| #' Returns an empty Enrichr results table. | ||
| # ' |
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There is an extra comment line with '# '' that should be '#'' to maintain consistent roxygen2 documentation formatting.
| # ' | |
| #' |
Added detailed description for functions and examples
@ktrns @andpet0101 have a look