Dev#43
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Add unified GSEA plotting function and resolve documentation issues
Replace names of GSEA functions
Rename fdr_threshold to fdr_th in calc_jaccard
Fix parameter name for FDR threshold in Jaccard calculation in all lineas
Update network_clust parameters: Lower jaccard_threshold and min_degree for clustering
add: PA clustering functions: - list_gmts - calc_jaccard - do_clust - get_superterm - get_network_communities - network_clust - network_clust_gg add: - rmd files. add: Example datasets: - geneset_list - camera_results. add: Vignette: - pathway_analysis_clustering. updated - DESCRIPTION - NAMESPACE.
…LUAD example datasets: deseq2_results (21,330 genes), norm_counts and vst_counts (21,330 x 32 matrices) - Add data-raw/deseq2_results.R generation script - Add @examples to: nice_Volcano, nice_VSB, nice_PCA, nice_UMAP, nice_tSNE, detect_filter, add_annotations, save_results, split_cases, tpm, get_stars, power_analysis, get_annotations - Update DESCRIPTION: LazyDataCompression xz - Update NAMESPACE and man/
Feature/dea functions
- Add vignettes/DEA_workflow.Rmd: full DEA workflow vignette - Add vignettes/prerender_figures.R: script to generate figures - Add vignettes/figures/: pre-rendered PNG plots - Update @param in nice_Volcano, nice_VSB_DESeq2 and nice_VSB with get_annotations() tip - Add note for nice_VSB_DESeq2 in vignette
…ript - Add slot to power_analysis() return list if plot=TRUE - Update vignettes/prerender_figures.R to use result_power directly instead of rebuilding the ggplot from scratch
- nice_PCA, nice_UMAP, nice_tSNE, nice_Volcano, nice_VSB, nice_KM - power_analysis, get_annotations, add_annotations, tpm - detect_filter, get_stars, save_results, split_cases - Add @references for UMAP, tSNE, and TPM methods - Add @note to get_annotations (gene_length caveat) and tpm (DEA warning)
- Fix get_annotations: replace rowNames with row.names in write.csv
Feature/dea functions
New functions: - splot_PA: single-comparison patchwork plot (NES + FDR + MSigDB collections) - multiplot_PA: multi-comparison faceted barplot with comparison_order param - heatmap_PA: leading edge heatmaps from R objects - heatmap_path_PA: leading edge heatmaps from file paths - getgenesPA: extract leading edge or all genes per gene set - addgenesPA: append all_genes and/or le_genes columns to pa_data Updated: - merge_PA: add fdr_replace param, return data frame, validate Comparison column, fix globalVariables, improve documentation - plot_PA.R split into splot_PA + multiplot_PA - Simplified FDR: always computed internally as tmp_log10FDR
Updated functions (plot_PA.R): - getgenesPA: 'top'variable in genes parmater (user-defined rank-based fraction) - addgenesPA: append also top_genes columns to pa_data - heatmap_PA: add top_genes support in plot_genes parameter New example dataset (data-raw/gsea_results.R): - gsea_results: simulated merge_PA() output, 40 gene sets x 3 comparisons (TumorVsNormal, MetastasisVsNormal, MetastasisVsTumor), 3 collections (HALLMARK, KEGG, GO), ~60% FDR < 0.05 per comparison Documentation: - getgenesPA: add GSEA User Guide definition of tags, le vs top distinction, list_gmts reference in geneset_list param - addgenesPA: add top description - heatmap_PA: update examples using gsea_results and camera_results
… vignette - Rename calc_jaccard() to geneset_similarity() across all R sources - Rename vignettes/pathway_analysis_clustering.Rmd to PA_clustering.Rmd - Regenerate documentation via devtools::document()
- Configure GitHub Pages via usethis::use_pkgdown_github_pages()
Feature/pa functions
- Add URL to DESCRIPTION pointing to BigMindLab GitHub Pages - Add example datasets section to reference index in _pkgdown.yml - Fix GitHub icon aria-label
Feature/pa clustering
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