Changes in version 0.99.35 Metadata - Corrected the maintainer record in DESCRIPTION: the ORCID 0000-0002-1825-0097 belonged to ORCID's fictional demo account (Josiah Carberry) and has been replaced with the author's real ORCID 0000-0002-2616-5132. The author field now uses the author's real name (Shenhui Xu, role aut + cre, unchanged email) instead of the placeholder "Dudali Lab" persona, in line with Bioconductor's guidance that the maintainer be an identifiable individual. No code or data changes. - Added contributor and reviewer credits in DESCRIPTION Authors@R: Yuanhang Zhao (ctb) and Mireia Ramos-Rodríguez (rev, Bioconductor reviewer of the initial submission, see https://github.com/mireia-bioinfo). Changes in version 0.99.34 Reproducibility - batch_calc_gsea() gains a seed argument (default 123) that makes GSEA results fully reproducible, fixing an upstream regression that affected all Bioconductor 3.23 users. Since clusterProfiler 4.19.3 the GSEA() engine switched to enrichit, and in 4.20.0 (the Bioc 3.23 release) the seed argument is silently dropped: it lands in ... and is never forwarded to enrichit::gsea_gson(), so the multilevel permutation engine draws a fresh seed from the worker R RNG on every call. Combined with future_lapply(future.seed = TRUE) deriving its worker seed stream from the main-session RNG state at call time, running the same data twice could flip borderline pathways across the significance cutoff (observed p-value drift up to ±0.016), reproducing the "same code, different pathway counts" issue reported for clusterProfiler 4.20.0. - Each contrast now derives its own deterministic seed from (seed, alphabetical rank of the contrast id) via the new internal helper .derive_task_seed(). Seeding is applied inside the future worker with withr::local_seed() (which restores the caller's RNG state on exit, per reviewer guidance against bare set.seed()), and the derived seed is also forwarded as clusterProfiler::GSEA(seed = ...): on clusterProfiler <= 4.20.x the local_seed() guarantees reproducibility, and once clusterProfiler >= 4.21.1 restores the seed argument (devel NEWS, 2026-08-14) the forwarded seed takes over natively. Results are identical across repeated runs and independent of workers and chunk_size, so a re-run on a different machine core count yields the same pathways. - The effective seed is recorded in the returned capsule (metadata$parameters$seed) for provenance. Set seed = NULL to restore the previous native (non-reproducible) engine sampling. Note that results produced before this fix, or under different clusterProfiler engine generations, will differ from the new deterministic output; this one-time shift is unavoidable and is the cost of stable results going forward. Changes in version 0.99.33 Bioconductor Review - Removed LazyData: true and LazyDataCompression: xz from DESCRIPTION per Bioconductor reviewer guidance (mireia-bioinfo). Bioconductor discourages LazyData because it implicitly injects data/ objects into the user's environment on package attach, obscuring data provenance and violating reproducibility principles. All package vignettes already use explicit data(x, package = "GSEAlens") calls, so this change has zero functional impact. Visualization - Unified the plotly DotPlot colorscale direction with the static generate_dotplot_code() ggplot2 export. Previously the interactive preview used forward viridis-D (high value = bright yellow) while the exported PDF used scale_fill_viridis_c(direction = -1) (high value = dark purple), producing mirror-opposite colors for the same pathway. The plotly colorscale is now reversed to match the export. - Removed hardcoded "(viridis)" suffix from the generate_dotplot_code() subtitle template. The export modal's Color palette dropdown already supports Viridis-D / Viridis-C / Magma / Inferno via dynamic scale_fill_viridis_c(option = ...) injection, so the static "(viridis)" label was misleading when a non-viridis palette was selected. Changes in version 0.99.32 Visualization - Fixed Joint Canvas (Tab 6) outer-margin leak. The user-adjustable "Canvas Margin" was previously applied via patchwork's & operator in R/14_shiny_mod_joint_canvas.R, which propagates theme() to every sub-plot. This overwrote the per-panel plot.margin = 0 set in vis-gsea-core.R and re-inflated the gaps between Panel 1 (RES curve), Panel 2 (hit strips), and Panel 3 (ranked list) inside each contrast's GSEA plot by ~30% of Panel 2's height. It also caused a visible mismatch between the Shiny preview (loose) and the Copy R Code standalone rendering (tight, since the copied code did not carry the & post-processing). - Fix: wrap the canvas in patchwork::wrap_elements(full = ...) before adding the outer theme(plot.margin = ...), so the margin only pads the canvas as a whole. Mirrored the same wrap_elements step in the Copy R Code output (generate_joint_canvas_code in R/15_code_generator.R) so the two paths render identically. - Visual verification: P1<->P2 gap ~30% -> ~10% of Panel 2 height; P2<->P3 gap ~32% -> ~12%. Shiny preview vs Copy R Code standalone now at ~98% visual parity. Changes in version 0.99.31 Visualization - Tightened vertical spacing in plot_directional_gsea Combined Pathway Plotting and Joint Canvas outputs. Previously the gene-hit strip panel (Panel 2) was visually floating between the running-score curve (Panel 1) and the ranked-list bars (Panel 3), with gaps as large as Panel 2's own height. Root cause: the plot.margin and heights parameters, inherited unchanged from the GseaVis internalization (fe8b2a6), were tuned for single-pathway GSEA and never revisited for the multi-pathway facet_wrap case. - R/06_visualization.R: heights is now n_lines-aware. Single pathway keeps the classic c(0.5, 0.2, 0.3); multi-pathway uses c(0.45, 0.30, 0.25) so each Panel 2 facet gets usable height. - R/vis-gsea-core.R: Panel 1, Panel 2, and Panel 3 plot.margin t/b are now all 0 (previously t=0.2 / b=0.2 / t=-0.1). Panel 2 panel.spacing is now unit(0, "cm") so multi-pathway facets abut. Removes the preview-vs-export discrepancy where the Shiny renderPlot preview looked tight but ggsave output carried inflated whitespace. Vignettes - Added a global knitr::opts_chunk$set(message=FALSE, warning=FALSE) setup chunk to GSEAlens.Rmd and GSEAlens-vignette-zh.Rmd, matching the preprocessing vignettes which already had it. Eliminated ~46 package-loading message blocks (## Loading required package: ...) per main vignette in the rendered HTML. Only the sessionInfo() output under "Session Info" is preserved, as required by Bioconductor. - Compacted fragmented markdown tables and merged thin consecutive code chunks across all four vignettes for cleaner HTML rendering. - Removed misused markdown blockquote (> **Note**: ...) patterns that rendered as fragmenting blockquotes in the HTML output. - Removed double-spacing inside code chunks and collapsed excessive blank lines that fragmented paragraphs. Changes in version 0.99.30 Addressed Bioconductor reviewer (mireia-bioinfo) round 2 comments on Bioconductor/Contributions #4251. Man pages - Replaced \dontrun with \donttest where possible so that R CMD check validates example syntax. Affected: build_gsea_pathways, generate_gsea_html_report, generate_joint_canvas_code, generate_boxplot_data_code, generate_boxplot_image_code. - For build_gsea_pathways, kept \dontrun only for the interactive menu() path and the auto_select = "ALL" path (downloads the entire MSigDB, slow). The non-interactive auto_select = c("H", ...) paths now use \donttest. - Added runnable \donttest{} examples for generate_gsea_html_report and generate_joint_canvas_code using the precomputed_gseares data object. - Added package-level man page (GSEAlens-package), reachable via ?GSEAlens or ?GSEAlens-package, listing main entry points (setup_gsea_env, batch_calc_gsea, build_gsea_pathways, extract_gsea_task) and the Shiny app launcher (launch_gsea_app). Data - Migrated six .rds files from inst/extdata/ to data/ and converted to .rda format so they can be loaded via data(). Affected objects: precomputed_gseares, preprocessed_dds, preprocessed_dds_se, preprocessed_limma, gsea_pathwaysets_toy, gsea_pathwaysets_toy_hallmark. - pathway_annotations.csv retained in inst/extdata/ (raw CSV per Bioconductor guidelines). - Set LazyData: true in DESCRIPTION for faster package load. - Added roxygen documentation for all six data objects (now accessible via ?precomputed_gseares etc.). - Added inst/scripts/convert_data_to_rda.R for converting .rds intermediates to .rda after regeneration. - Updated vignettes and examples to load data via data() instead of readRDS(system.file("extdata", ...)). Vignettes - Removed redundant GSEAlens:: prefixes from both main vignettes (GSEAlens.Rmd and GSEAlens-vignette-zh.Rmd); 18 occurrences cleaned. - Fixed vignette YAML rendering failure: the YAML frontmatter contained blank lines between every field, which broke the vignette: > folded scalar (per YAML spec, blank lines inside a folded scalar are preserved as newlines, causing the %\VignetteEngine{...} directive to be split and knitr to fail parsing the frontmatter). All four .Rmd files now have compact YAML headers. BiocCheck hygiene - Removed GSEAlens.BiocCheck/ directory from the package source tree (was causing "Remove 'GSEAlens.BiocCheck' from the package directory" ERROR). Changes in version 0.99.29 Fix mode_select FDR filter: user-selected pathways no longer silently dropped. candidate_filtered() in R/13 (dotplot/network) and R/16 (hubgene vis) applied p.adjust < fdr_threshold even in mode_select mode (user picked from Main Table), silently dropping pathways with p.adjust >= 0.25. Example: KOHN_EMT_MESENCHYMAL (p.adjust = 0.30 in RZ_vs_RT contrast) was invisible in the DotPlot despite being explicitly selected. Fix: mode_select skips FDR filter (user intent priority); mode_topN keeps automatic FDR filtering. Status messages updated to show "no FDR filter" in mode_select mode to avoid misleading labels. Changes in version 0.99.28 Export code: pass figure dimensions (Width/Height) to ggsave. The "Width (inch)" and "Height (inch)" inputs in the Dimensions section of each export modal were not propagated to the generated code's ggsave() lines — they used hardcoded defaults. Fixed by adding fig_width and fig_height parameters to all 5 publication plot generators (generate_dotplot_code(), generate_volcano_code(), generate_de_volcano_code(), generate_network_code(), generate_hubgene_code()), and passing input$exp_width / input$exp_height (and module-specific variants) from R/10, R/13, and R/16. Changes in version 0.99.27 Export code: unified save options (PDF + PNG + SVG). All publication plot code generators now consistently include three commented-out ggsave() lines covering PDF, PNG, and SVG output formats. Previously the save blocks were inconsistent — some had only PDF, some had PDF + PNG, and only one had all three. Changes in version 0.99.26 Code style: convert 2-space indentation to 4-space across all R files. BiocCheck reported 6566 lines with non-4-space-multiple indentation. Fixed by converting all 2-space indentation to 4-space (multiplying leading whitespace by 2) across 24 R files (6371 lines fixed). After fix: 0 lines with non-4-space indentation in source R files (BiocCheck may still report a small number from cached .Rproj.user files, which are not part of the package source). \dontrun tags kept as-is (8 occurrences): all examples reference external data files or interactive menus, so \donttest would cause R CMD check WARNINGs. BiocCheck NOTE is acceptable. Changes in version 0.99.25 R CMD check / BiocCheck compliance: - DESCRIPTION: Added explicit Author and Maintainer fields (required by R 4.6.0's R CMD check, which no longer auto-derives them from Authors@R alone). Added family = "Lab" to person() calls. - Rd files: Regenerated all 5 publication plot generator Rd files via devtools::document() to include target_collection and margin parameters. Removed unused target_collection parameter from generate_de_volcano_code() (uses get_de_table(), not extract_gsea_task()). - R CMD check: 0 ERROR, 0 code/doc mismatch, 0 syntax error. Remaining 3 WARNINGs are non-code (.Rcheck residual, vignettes not compiled — resolved by R CMD build). - BiocCheck: 0 ERROR, 0 WARNING, 11 NOTEs (stylistic only). Changes in version 0.99.24 Joint Canvas: show pathway name in canvas title for single-pathway. The plot_annotation title previously showed "x pathways" even when only one pathway was selected. Now includes the formatted pathway name: - Multi: "Joint GSEA Canvas: 4 contrast groups x 3 pathways" - Single: "Joint GSEA Canvas: 4 contrast groups x 1 pathway (Interferon Alpha Response)" Changes in version 0.99.23 Joint Canvas: single-pathway label refined. v0.99.22 added a labs(subtitle) to p1 in plot_directional_gsea() when n_lines == 1, but this was redundant in the Joint Canvas where each sub-plot already has its own main_title. Reverted the subtitle approach. Instead, the Joint Canvas module (R/14) now includes the formatted pathway name directly in the main_title when only one pathway is selected: - Multi-pathway: "RT vs M [3 pathways]" (unchanged) - Single-pathway: "RT vs M: Interferon Alpha Response" Changes in version 0.99.22 Joint Canvas: label single-pathway plots. When only one pathway is plotted in the GSEA Joint Canvas (or any caller of plot_directional_gsea() that supplies a custom main_title), the pathway name was not displayed because the legend-override logic only ran for n_lines > 1, and the single-pathway path uses a gradient color scale (no discrete legend). Fixed by adding an else branch in plot_directional_gsea(): when n_lines == 1, the formatted pathway name is added as a labs(subtitle) on p1, mirroring the main-table behavior where the pathway name is shown as the title. Changes in version 0.99.21 Export code: respect user-selected gene-set collections. Previously all five publication plot code generators hardcoded target_collection = "ALL" in the exported extract_gsea_task() call, so the Pathway Volcano always showed all gene sets regardless of the collection filter selected in the data-prep module. Fixed by: - R/08 (mod_data_prep_server): process_data_core() now includes collections in its return list, propagating the user's selection. - R/15: generate_volcano_code(), generate_dotplot_code(), generate_network_code(), and generate_hubgene_code() accept a new target_collection parameter (default "ALL") and emit it into the generated R code. generate_de_volcano_code() is unaffected (uses get_de_table(), not extract_gsea_task()). - R/10 (mod_quadrant_server): passes data_list$collections to generate_volcano_code(). - R/13 (mod_pathway_relation_server): passes data_list$collections to generate_dotplot_code() and generate_network_code(). - R/16 (mod_hubgene_vis_server): passes data_list$collections to generate_hubgene_code(). Now: selecting "H" produces target_collection = c("H"), selecting "C2" + "C2:CP" produces target_collection = c("C2", "C2:CP"), and the exported Pathway Volcano only plots pathways within the selected collection(s). Changes in version 0.99.20 DotPlot direction annotation: move labels outside the plot panel border. The previous fix (v0.99.19, y=1.0 + just="top") placed the enriched-in labels inside the plot panel, causing them to be overlapped by data points. Fixed by: - y: 1.0 -> 1.01 (just above the top border, outside the panel). - just: "top" -> "bottom" (text grows upward from y=1.01 into the subtitle gap, sitting flush against the outside of the border). - subtitle margin(b): 22 -> 20 (tightened now that text direction is correct). Verified: labels render outside the border, flush against it, not overlapped by data points or subtitle, with default top margin (18pt). Changes in version 0.99.19 DotPlot direction annotation layout fix: the enriched-in labels (blue left / red right) previously overlapped with the subtitle because annotation_custom used y = 1.04 with just = "bottom", placing them at the same vertical position as the subtitle text. Fixed by: - Changing y from 1.04 to 1.0 (exact top of plot panel). - Changing just from "bottom" to "top" (text grows upward into the subtitle gap, not downward into the plot). - Increasing subtitle margin(b) from 14 to 22 (creates enough space for the 12pt annotation text between subtitle and plot panel). Verified with 20-pathway bidirectional data: no overlap between title, subtitle, and colored direction labels. Changes in version 0.99.18 DotPlot Canvas Margin fix + enriched-in direction annotation redesign: - Canvas Margin now effective: the four margin inputs (top / bottom / left / right) in mod_pathway_relation_server() are now passed through to generate_dotplot_code(), so changing them updates the live preview and exported code. Previously the dotplot branch of .current_export_code() omitted all margin arguments. - Direction annotation redesign: the verbose bottom caption ("Left (NES<0): Enriched in ... | Right (NES>0): Enriched in ...") is replaced by two concise colored labels rendered above the plot panel via annotation_custom(grid::textGrob(...)): - Left label in blue (#3B6EA5, bold) — NES<0 enrichment direction. - Right label in red (#C0392B, bold) — NES>0 enrichment direction. - Single-direction aware: if all selected pathways have the same NES sign, only one direction label is shown. - Plotly title simplified: the interactive DotPlot title also drops the "Left (NES<0):" / "Right (NES>0):" prefixes and uses colored elements for the enriched-in labels. Changes in version 0.99.17 Live-preview class-validation fix for DotPlot / Network / HubGene plots: the Shiny module eval environments in mod_pathway_relation_server() and mod_hubgene_vis_server() now inject the module-parameter gsea_res (consistent with the already-working mod_quadrant_server()) instead of data_prep_list$data()$gsea_res, which could lose its GseaRes class attribute through the reactive chain and trigger "Input object is not of class GseaRes" during extract_gsea_task(). Changes in version 0.99.16 Concise export-code refactor + DE Volcano layer ordering fix: 0 ERROR / 0 WARNING / 0 NOTE on R CMD check --no-manual (Status: OK); BiocCheck reports 0 ERRORS, 0 WARNINGS (support-site check excluded as external service). - Concise export code: five publication plot code generators (generate_dotplot_code(), generate_volcano_code(), generate_de_volcano_code(), generate_network_code(), generate_hubgene_code()) now produce concise scripts that assume a GseaRes object is loaded in the environment and derive plot data via extract_gsea_task() / get_core_genes_list() / get_de_table() / build_edge_list_safely() / build_hubgene_network(), replacing the previous verbose dput() data-literal approach. - DE Volcano layer ordering: the exported DE Volcano script now sorts points by a plot_order column (mirroring the interactive plotly) so that special-category genes (Pathway / Selected / Both) are drawn on top of significant and NS points, making them easy to spot. - Pathway DotPlot direction caption: both the exported ggplot2 script and the interactive plotly view now include a direction caption ("Left (NES<0): Enriched in [group] | Right (NES>0): Enriched in [group]"). Changes in version 0.99.15 Documentation completeness pass + dependency cleanup: 0 ERROR / 0 WARNING / 0 NOTE on R CMD check --no-manual (Status: OK); BiocCheck reports 0 ERRORS, 0 WARNINGS, 10 NOTES (all stylistic). - Removed unused shinytest2 from Suggests: the package was declared but had zero references in the entire codebase. On environments without shinytest2 installed, R CMD check would ERROR at the dependency-check stage. - Complete @param documentation: added missing @param tags for margin_top/bottom/left/right, show_annotations, n_selected, selected_ids, and verbose across 6 functions (fixes R CMD check WARNING on Rd \usage sections). - Runnable examples for all generate_*_code() functions: converted all \dontrun{} to \donttest{} and added inline-data examples to generate_combined_plot_code(), generate_dotplot_code(), generate_volcano_code(), generate_de_volcano_code(), generate_network_code(), and generate_hubgene_code() (fixes BiocCheck ERROR on man-page runnable-example coverage). - DotPlot scale fix: removed sqrt transform and fixed limits from scale_size_continuous() — now uses data-driven domain (no limits, no transform), matching enrichplot::dotplot convention exactly. - Live Preview (WYSIWYG): all image export modals now include a real-time preview pane so users can see render results before export. - Unified code export: Combined Pathway Plotting and Joint Canvas code export is now integrated into the image export modal ("Copy R Code" button), replacing standalone code-export buttons. - Pathway Volcano labels: changed "Up in [group]" to "Enriched in [group]" to align with GSEA enrichment semantics. - Vignettes updated (EN + ZH): dotplot description, Combined Pathway Plotting, Joint Canvas, and Reproducible Code Export sections all reflect the latest module behavior. Changes in version 0.99.14 Bioconductor re-review preparation: 0 ERROR / 0 WARNING / 0 NOTE on R CMD check --no-manual (Status: OK); BiocCheck reports 0 ERRORS, 0 WARNINGS, 10 NOTES. All reviewer comments are now addressed point-by-point (see 2026_06_26_biocondutor审查意见/2026_07_05_待回复的中文审查意见.md). - Runnable examples for all exported functions: removed \donttest{} from batch_calc_gsea.Rd and replaced \dontrun{} in plot_gsea_memory.Rd with an inline synthetic data.frame; added self-contained runnable examples to all 8 generate_*_code() functions (using precomputed_gseares.rds or inline mini data). - Slimmed preprocessed_dds_se.rds: 8.05 MB -> 3.05 MB (-62%) by dropping DESeq() intermediate assays (mu/H/cooks), flattening GRangesList to GRanges, and removing 5 Ensembl coordinate columns. DESeq2::results() output is bit-identical before/after. - DESCRIPTION Authors@R: switched to single-line format to fix DCF parsing; removed redundant Author/Maintainer fields per BiocCheck. - batch_calc_gsea() defaults: workers default reduced from 4 to 2 for Bioconductor build machine compatibility; output_dir default changed to tempdir(); future::plan() is now saved and restored via on.exit() to avoid global state pollution. - Vignette workers: all batch_calc_gsea() calls in both English and Chinese vignettes updated to workers = 2. - Vignette transparency note: added "Note on the shipped dds_se" block in both EN/ZH vignettes explaining the slimming rationale. Changes in version 0.99.13 Bioconductor submission preparation: 0 ERROR / 0 WARNING / 0 NOTE on R CMD check --as-cran (Status: OK). All P0/P1/P2 issues from the 2026-07-01 in-house code-bug audit are resolved; four report items were verified as mis-diagnoses (Authors@R parse error is a loadNamespace flakiness in R 4.6.0 not a CRLF issue; Chinese comments are already valid UTF-8, not GB18030; enrichit 0.1.4 is on CRAN; clusterProfiler no longer re-exports gseaScores so the direct enrichit::gseaScores import is the correct path). Full diff and rationale in 2026_06_26_GSEAlens辅助开发文件夹/2026_07_01_GSEAlens代码Bug排查与修复_实施报告.md. - CRLF -> LF (123 files): bulk-converted R/*.R, inst/scripts/*.R, man/*.Rd, tests/testthat/*.R, vignettes/*.Rmd, plus DESCRIPTION / NAMESPACE / LICENSE / LICENSE.md / NEWS.md. LF-only line endings are required by Bioconductor; added a .gitattributes to lock the policy so Windows git will not silently convert back on checkout. - DESCRIPTION tidy: removed the field-separator blank lines that Bioc strict-DCF requires to be absent; collapsed the multi-line Imports: and Suggests: continuations to single-line comma lists (the previous Imports: \n\n value1, form triggered "Found continuation line starting ... at begin of record" at build time). - Suggests: ggrepel: added explicitly even though the package is already pulled in transitively via enrichplot, so reviewers and R CMD check see the dependency for the publication-export code that emits ggrepel::geom_label_repel / geom_text_repel. - Dead code removed (B-1): R/04_calculation.R had a geneset_species <- gsea_env$geneset$species %||% "HS" line inside a future_lapply worker that (1) was never read after assignment and (2) reached gsea_env via implicit globals capture rather than the explicit worker arguments. Deleted and replaced with a 3-line explanatory comment. - setwd / tryCatch/finally -> withr::local_dir (B-2): R/06_visualization.R HTML-report saveWidget block now uses withr::local_dir(bundle_dir) so an error in saveWidget cannot leave the session in a half-changed working directory. - png + ComplexHeatmap::draw -> png + on.exit(dev.off()) + draw (C-3): same file, row-heatmap block. If draw() errors, the residual png device used to swallow every subsequent plot; the on.exit guard guarantees dev.off() runs on any exit path. - .Rbuildignore expanded (B-3): added tools, .Rhistory, .RData, .Ruserdata, README.html, .history, *.log, IDEA.md, .github to match the actual non-build artefacts in the repo (notably IDEA.md in the project root, which would otherwise have been packaged). - **%||% unified to rlang::%||%(B-4 / B-6)**: removed the package-localif (!exists("%||%", ...))definition fromR/01_backends.R. The local version had a different semantics (it also fell back on all(is.na(x))andlength(x) == 0), which was the latent bug behind B-6. Added #' @importFrom rlang %||%`` in R/utils-imports.Rand the correspondingimportFrom(rlang,%||%)inNAMESPACE`. - dplyr::all_of -> dplyr::any_of (B-5): R/03_pathways.R TERM2NAME select for Collection / Subcollection columns uses any_of() so an msigdbr snapshot that lacks gs_collection / gs_subcollection no longer hard-errors. - Defensive S4 dispatch in inspect_gsea_res (B-7): R/05_extraction.R task$data@result$p.adjust access is now guarded by methods::is(task$data, "gseaResult") with fallbacks for data.frame shapes (p.adjust or padj columns) and a safe NA_integer_ default. Avoids @ on non-S4 objects if a future backend returns a plain frame. - setup_gsea_env(verbose = TRUE) (D-2): new optional argument gating the top-level message() calls. Lower-level detection messages stay un-gated. Rd documentation updated to match. - counts() -> DESeq2::counts() (D-4): R/01_backends.R DESeq2 branch now namespaces the call so it cannot collide with Matrix::counts() or any other package that might re-export a counts symbol. - Rd documentation sync: man/setup_gsea_env.Rd, man/generate_volcano_code.Rd, and man/generate_de_volcano_code.Rd updated to reflect the new verbose, n_selected, selected_ids, and show_annotations arguments (the latter two had drifted from the actual R signatures after the 0.99.12 ggrepel work). - .gitattributes added: forces eol=lf for *.R, *.Rmd, *.Rd, DESCRIPTION, NAMESPACE, LICENSE, LICENSE.md, NEWS.md. Prevents Windows git autocrlf from re-CRLF'ing the package on every checkout. Changes in version 0.99.12 Publication export fidelity: ggrepel labels for volcano exports, new boxplot image export modal, modal scroll fix, and checkbox-driven annotation toggles. - Volcano export labels (R/15_code_generator.R, R/10): generate_volcano_code() now accepts selected_ids and annotates the user-selected pathways with ggrepel::geom_label_repel (orange labels mirroring the interactive plotly selection). generate_de_volcano_code() annotates user / pathway / both genes (green / orange / purple labels) the same way. Labels use max.overlaps = Inf so all selected points are named. - Checkbox-driven annotations (R/10, R/15): both volcano export modals gain a checkbox (default unchecked). Pathway Volcano: "Show stats subtitle"; DE Volcano: "Show stats + direction banners". When unchecked the figure is clean (title + axes only, identical to pre-annotation behavior); when checked, subtitle shows the same statistics as the interactive plotly title and DE Volcano adds red "High in " / blue "High in " corner banners using the actual group names. - Boxplot image export (R/10, R/15): add an "Export Publication Plot" button to panel 4 (Full Expression Distribution) of the Quadrant module, opening a full export modal (PDF/PNG/SVG/TIFF + Live Preview + Copy R Code). New generator generate_boxplot_image_code() produces a self-contained ggplot2 script reproducing the interactive plotly boxplot (boxplot + jitter, group colors, optional zero baseline, optional custom group order). - Modal scroll fix (R/07_shiny_app.R): replace the single max-height: 85vh on .modal-body with a flex layout (.modal scrolling viewport, .modal-content bounded to 92vh flex column, pinned header/footer, scrolling body). Fixes the bug where a tall Live Preview pushed the modal header above the fold and the scrollbar could not reach it. - DotPlot export subtitle (R/15): dynamic subtitle now references the active Color by / Size by selection instead of the previous hardcoded string. - DotPlot export missing bubbles (R/15_code_generator.R): fix silent data loss in the Pathway DotPlot Live Preview and PDF/PNG export. generate_dotplot_code() emitted scale_size_continuous(limits = c(0, 50/500), trans = "sqrt"), but ggplot2 4.x removed the oob argument from scale_*_continuous, so any pathway with CoreCount > 50 (core_size mode) or setSize > 500 (setsize mode) was silently censored at render time — the corresponding bubbles vanished from the figure and the only signal was a stderr warning ("Removed N rows containing missing values or values outside the scale range") that the Live Preview pane does not surface. This was misperceived as "long pathway names dropping bubbles" because large gene sets tend to also have long names. The interactive plotly view never had the bug (it clamps via pmin/pmax). Fix: clamp the active size column to the scale limits in the data preprocessing stage (mirroring the plotly path) so limits becomes a pure visual-range anchor and never a censoring gate. Also migrate the deprecated trans = "sqrt" argument to transform = "sqrt" to clear the ggplot2 4.x deprecation warning. Verified end-to-end with 9 MSigDB-style pathways (setSize 80–1800, CoreCount 8–95, names up to 60 chars): all 9 bubbles render in all 4 size/color combinations with zero censoring warnings. - DE Volcano export code generator (R/10_shiny_mod_quadrant.R): fix wrong generator invocation in the Quadrant module's DE Volcano "Export Publication Plot" path. The reactive was calling generate_boxplot_image_code() (a boxplot-specific generator) with boxplot-shaped arguments, producing an R script that did not reproduce the interactive DE Volcano. Switched to generate_de_volcano_code() with the correct arguments (user_genes, pathway_genes, logfc_thresh, pval_thresh, show_annotations) sourced from the matching reactive values (highlight_genes_reactive(), selected_pathway_genes(), input$de_exp_logfc, input$de_exp_pval, input$de_exp_show_stats). The clipboard-copied R code now matches the Live Preview and the downloaded PDF/PNG. Changes in version 0.99.11 Visualization fidelity and publication export. Brings the interactive plotly/visNetwork figures in line with enrichplot / clusterProfiler conventions, and adds a unified "Export Publication Plot" workflow that produces both static ggplot2 images and reproducible R scripts. - DotPlot size mapping (R/13_shiny_mod_pathway_relation.R): replace per-render min-max normalization with a fixed-domain + sqrt scale (CoreCount domain [0, 50], setSize domain [0, 500]), matching ggplot2::scale_size_continuous(range=...) semantics. The previous normalization pinned min/max to fixed pixel sizes every render, hiding the magnitude difference between CoreCount (typical 5-50) and setSize (typical 50-500), so switching "Size by" produced visually identical dot patterns. The new scale also makes dot sizes comparable across FDR/TopN parameter changes. DotPlot hover text now shows both dimensions, with the currently-driven one bolded, plus P-value. - Pathway Volcano Y axis (R/10_shiny_mod_quadrant.R): switch from -log10(p.adjust) to -log10(pvalue), matching the EnhancedVolcano / clusterProfiler convention. P-value (rather than FDR) provides the sensitivity needed to expose gradient structure in marginal pathways; FDR compresses most points to the bottom. Hover text and title updated accordingly. - Network edge width (R/13_shiny_mod_pathway_relation.R): add a user-selectable Edge Width Mode dropdown with two options: Weight-based (default; edge width linearly proportional to Jaccard value, emapplot convention, faithful to similarity magnitude) and Rank-based (legacy behavior; edge width assigned by Jaccard rank for uniform visual spacing). The default Weight-based mode is the standard for publication figures; the Rank-based mode is retained for dense networks with low weight variance. - HubGene pathway node size (R/16_shiny_mod_hubgene_vis.R): add a Pathway Node Size Encoding dropdown with three modes: By gene-set size (setSize, default; matches enrichplot::cnetplot convention, sqrt-scaled), By significance (-log10(FDR)), and Fixed size (legacy slider-only behavior). The slider value acts as the base size; the chosen encoding scales within [0.6x, 1.4x] to keep visNetwork's force-directed layout stable (variance beyond ~2.3x causes layout jitter). Gene-node sizing is unaffected. Pathway hover text now also shows setSize. - Export Center (R/13, R/10, R/16, R/15): add a unified "Export Publication Plot" modal to the DotPlot/Network/Volcano/HubGene panels. Provides width/height/DPI/format (PDF, PNG, SVG, TIFF) controls and two actions: (1) download a static ggplot2-rendered image via ggsave (zero external dependencies; no kaleido/orca required, unlike plotly::save_image); (2) copy a fully reproducible R script to the clipboard via clipr. Four new exported code generators in R/15_code_generator.R: generate_dotplot_code(), generate_volcano_code(), generate_network_code(), generate_hubgene_code(). Network and HubGene static renderings use igraph layouts + base ggplot2 (no ggraph dependency, which is not in DESCRIPTION). - Update English and Chinese vignettes (Tab 3 and Tab 4 sections) to document the new sub-panels, encoding modes, and export workflow. Changes in version 0.99.10 BiocCheck compliance: clear the ">= 80% runnable examples" ERROR, plus provenance documentation for shipped pre-computed RDS objects. - Convert 10 exported functions from \dontrun{} examples to truly runnable examples by loading shipped pre-computed RDS objects (precomputed_gseares.rds, preprocessed_limma.rds, gsea_pathwaysets_toy.rds) or writing demo files to tempdir(). Functions updated: setup_gsea_env, inspect_gsea_env, import_gsea_capsule, plot_directional_gsea, generate_pathway_plot_code, build_hubgene_network, extract_hub_genes, read_addition_data, creat_addition_data_rdsfile, create_addition_template. This raises runnable example coverage from 57% (21/37) to 84% (31/37) and clears the BiocCheck ERROR "At least 80% of man pages documenting exported objects must have runnable examples". - Fix BiocCheck WARNING on man/visualization.Rd: the roxygen block for the visualization documentation landing page had a duplicate @name / NULL section, which suppressed the \value{} block and left the Rd without a value section. Consolidated to a single roxygen block with @return NULL so the generated Rd has a proper \value{}. - Fix BiocCheck NOTE "Use accessors; don't access S4 class slots via '@' in examples": replaced task$gsea_res@result$ID[1] with as.data.frame(task$gsea_res)$ID[1] in get_core_genes_for_pathway() and get_core_genes_list() examples (R/utils-core-genes.R). The clusterProfiler::gseaResult class has an as.data.frame() method that exposes the @result slot without direct S4 slot access. - Add inst/scripts/make_precomputed_gseares.R, the maintainer-only generator script for inst/extdata/precomputed_gseares.rds. Documents the exact inputs (preprocessed_limma.rds + gsea_pathwaysets_toy.rds), clusterProfiler/fgsea versions, and the batch_calc_gsea() call used to produce the shipped object, so the artefact is reproducible when upstream packages bump. Update inst/scripts/README.md with the new file's row in the regeneration table and the dependency order note. - Remove stale tests/testthat/test-run_app.R.placeholder.bak (renamed backup of the placeholder test retired in 0.99.9). Remove misspelled GSEAlen.Rproj (duplicate of GSEAlens.Rproj); also drop its line from .Rbuildignore. Changes in version 0.99.9 Bioconductor review Phase 4: dependency hygiene, import hardening, and the first real test suite. - Replace parallel::detectCores() with future::availableCores() in batch_calc_gsea() (R/04_calculation.R) so that the worker count honors future backend configuration (e.g. future.cores option, CIRCLE_NODE_TOTAL, Slurm env vars) instead of always reading hardware cores. This removes the last direct parallel:: call from the package and aligns with Bioconductor guidance to defer parallelization decisions to the user-selected backend (future / BiocParallel). - Replace plyr::rbind.fill() with dplyr::bind_rows() in build_hubgene_network() (R/utils_hubgene.R). The two are semantically equivalent for the homogeneous data-frame list used here (both fill missing columns with NA), but dplyr::bind_rows() is actively maintained and avoids the superseded plyr dependency. Verified behavior parity with a targeted R check on heterogeneous-column inputs. - Move withr from Suggests to Imports and add explicit importFrom(withr, with_seed) / importFrom(withr, local_seed) to NAMESPACE. withr is now used unconditionally in production code (RNG scoping in 4 sites since 0.99.7), so it must be a hard dependency. - Add 23 explicit importFrom declarations covering tools (1), withr (2), enrichit (1), igraph (7), visNetwork (8), shinyjs (2), and progressr (2) to NAMESPACE via R/utils-imports.R. This eliminates all residual pkg::fun() calls for these packages so that R CMD check reports zero "undeclared package usage" notes and downstream code is robust to masked search-path changes. - Add the first real testthat suite: 73 tests across 6 files (tests/testthat/test-calculate_overlap_ratio.R, test-color_by_direction.R, test-build_edge_list_safely.R, test-validate_param.R, test-build_gsea_pathways.R, test-setup_gsea_env.R). The previous test-run_app.R placeholder (expect_equal(2 * 2, 4), unchanged since v0.99.0) is preserved as .placeholder.bak. The new suite covers 5 exported functions and the setup_gsea_env() input-validation gateway; all tests pass cleanly under R CMD check --as-cran. Closes Bioconductor reviewer comment #11 ("add real tests"). - Wrap the two interactive build_gsea_pathways() examples (those relying on readline()) in \dontrun{} and correct the MM-species example to use the M-prefixed collection codes (c("MH", "M5:GO:BP")) instead of the human codes. This resolves a long-standing R CMD check ERROR where the example called readline() in a non-interactive session. - Translate 7 Chinese code comments in R/09_shiny_mod_table.R (JS debounce logic and Shiny input-handler semantics) to English to eliminate the R CMD check "non-ASCII characters in R code" WARNING. Changes in version 0.99.8 Follow-up hardening to the scoped RNG work in 0.99.7; no user-facing behavior change. - Fix a stale comment in prepare_hubgene_nodes() (R/utils_hubgene.R) that claimed default 123 for the seed parameter while the function signature is seed = 42. The comment now reads default 42, matching the documented @param seed default and the Shiny UI numericInput(vis_seed, value = 42). - Add a defensive NULL fallback for input$seed in the pathway-relation rendering reactive (R/13_shiny_mod_pathway_relation.R). During fast reactive invalidation the Shiny numericInput can transiently be NULL before its value settles; the renderer now falls back to 42L so that withr::with_seed() always receives an integer, preventing a spurious "default" layout calculation failed message. This complements the analogous guard already present in R/16_shiny_mod_hubgene_vis.R. Changes in version 0.99.7 Bioconductor review Phase 3 completion: scoped RNG, scope-safe mutation, defensive future cleanup. - Replace all 4 set.seed() calls with withr::local_seed() / withr::with_seed() so that stochastic igraph layouts (Fruchterman-Reingold) remain reproducible without polluting the caller's global RNG state. Locations: R/08_shiny_mod_data_prep.R (permutation sampling), R/13_shiny_mod_pathway_relation.R (network layout, 2 sites), R/utils_hubgene.R (hubgene layout). The seed parameters remain exposed to users (function seed argument, Shiny input$seed). withr is now in Suggests. - Remove all 3 <<- super-assignments. In R/08_shiny_mod_data_prep.R the recursive permutation builder now uses an explicit new.env() accumulator. In R/13_shiny_mod_pathway_relation.R the edge_list and node_df module-scope variables become shiny::reactiveVal() objects: output$plot_network writes via edge_list_rv(...) / node_df_rv(...), and observeEvent(input$show_edge_detail) reads via edge_list_rv(). This fixes a latent race condition where the observer could read NULL or a stale edge list during async re-rendering; it now degrades gracefully with a "Network is still being computed" notification. - Harden the future parallel backend lifecycle in batch_calc_gsea(). options(future.globals.maxSize = ...) and future::plan(future::multisession, ...) are now wrapped in on.exit() so the user's original options and sequential plan are restored even if future.apply::future_lapply() errors out. The trailing future::plan(future::sequential) line is removed (now handled by on.exit). future + future.apply are retained (not switched to BiocParallel) because GSEAlens routinely serializes > 2 GB of globals (DE table + gene set dictionary + metadata dictionary) on Windows, where BiocParallel::SnowParam PSOCK serialization was measured to be 3-5x slower than future::multisession for this workload; see Phase3 专项深度分析 report for the benchmark rationale. Changes in version 0.99.6 Bioconductor review Phase 3 partial: code quality optimizations addressing reviewer comments on pipe operator, signal conditions, and suppressWarnings. - Replace all magrittr %>% pipe operators with native R pipe |> across the entire R/ directory (~90 occurrences in 10 files). Remove the magrittr import from DESCRIPTION, drop export("%>%") and importFrom(magrittr, "%>%") from NAMESPACE, and delete R/utils-pipe.R and man/pipe.Rd. This eliminates an unnecessary dependency and aligns with modern R (>= 4.1) best practices. - Restructure error and warning signals to use rlang::abort() / rlang::warn() with structured condition classes throughout R/00_class_validations.R (9 signals) and R/utils-accessors.R (30 signals). Each signal now carries a .class suffix (e.g. "GSEAlens_limma_intercept_detected", "GSEAlens_contrast_not_found") for programmatic handling via tryCatch(). Removed redundant [SampleMeta], [GeneDetector], [SymbolMap], [Limma Warning], [DESeq2 Warning] prefixes from warning text; these categories are now expressed through the condition class instead. - Refactor validate_param() in R/utils-core-genes.R to avoid unnecessary suppressWarnings() when input is already numeric. The function now checks is.numeric(value) first and only falls back to suppressWarnings(as.numeric(...)) for string inputs, removing the silent-coercion warning suppression for the common numeric case. - Vignette reshaping (continued from 0.99.5): split English/Chinese vignettes into a main GSEAlens.Rmd / GSEAlens-vignette-zh.Rmd plus supplementary preprocessing vignettes (GSEAlens-preprocessing.Rmd / GSEAlens-preprocessing-zh.Rmd). Main vignettes now focus on GSEAlens core functionality and add a detailed Shiny app exploration section. All vignettes switched to BiocStyle::html_document output, @-slot access replaced with SummarizedExperiment accessors, and batch_calc_gsea() examples write to tempdir(). Changes in version 0.99.5 - Fix "plotting error: missing value where TRUE/FALSE needed" when switching gene set subgroup (e.g. H -> C2/C5) with stale pathway selections in Joint Plot and Multi-Plot modules. Add defensive guard in plot_directional_gsea() to validate pathway IDs against the active GSEA result, and add null check in .gs_info() for missing gene sets. - Enable cross-collection pathway overlay in Multi-Plot (combined pathway plotting). Multi-Plot now uses the full gsea_res (all gene set collections) instead of the sliced subset, allowing pathways from different collections (e.g. H + C2) to be plotted together on the same enrichment chart, consistent with Joint Canvas behavior. - Fix UTF-8 BOM (Byte Order Mark) encoding in R source files that caused parse() failures on strict parsers. All R/*.R files now use clean UTF-8 without BOM, aligning with R package best practices and BiocCheck requirements (LEVEL: WARNING on BOM-annotated files). Changes in version 0.99.4 - Replace the "Export Boxplot Data Code" button in the Quadrant module (panel 4 "Full Expression Distribution") with an "Export Boxplot Data" modal that directly shows the per-sample expression values in two tab-separated formats: wide (first row = sample IDs, second row = gene expression values, left-most cell = gene name) and long (one row per sample with Sample / Group / Expression). Each table has Copy-to-Clipboard and Download-CSV controls. The previous R-code generator generate_boxplot_data_code() is retained for backward compatibility and export to a runnable R script. - Add "Export Boxplot Data Code" button to the Quadrant module (panel 4 "Full Expression Distribution"). Generates a self-contained R script that extracts the per-sample expression values (Sample / Group / Expression) of the currently selected gene so users can reproduce the boxplot in R, GraphPad, or Excel. New function generate_boxplot_data_code() is exported. - Fix BiocCheck warnings: replace sapply() with vapply(), 1:... with seq_len/seq_along - Fix R CMD check NOTEs: enrichit import, fc global variable, License stub - Add @return documentation to man pages - Fix vignette chunk labels - Replace cat()/print() with message() in inspect functions - Add comments to set.seed() and suppressWarnings() usage - Update installation method to use pak - Bump R version dependency to 4.6.0 - Add LICENSE.md for GitHub display Changes in version 0.99.0 - Pathway Network module addition - Hubgene Network module addition - AI prompt module addition - Script description standardization Changes in version 0.0.9 - Gene expression and plot code. Changes in version 0.0.8 - Repair data source of Heatmap in Limma-voom Changes in version 0.0.7 - Translate to EN. Changes in version 0.0.6.9000 - Update to the new parallel execution logic, and enable progressr as the progress bar. - Add external data to monitor system memory and CPU status and monitor the running status of the GSEAlens enrichment function. - Update on performance testing and monitoring when running GSEA detection. Changes in version 0.0.6 - Rectify the pairing issues between Ensembl IDs and SYMBOLs in the expression matrix. Changes in version 0.0.5 功能完善 - 已经可以使用的版本 - 交互与识别功能已经准备完全 待开发功能 - 一键输出选定图像的R代码功能。 Changes in version 0.0.4 多图交互 - 加入多种额外添加图像，首次完成同页面多组结果交互。 Changes in version 0.0.3 双接口 - 可接受deseq2数据制图 Changes in version 0.0.2 初版可交互 - 对接limma-voom，可视化功能初步完成。 Changes in version 0.0.1 国科金开发版本 - 最开始的原初版本，完成了国科金标书中生信部分的图像制作