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enrichplot 1.99.7.9001

  • Align import_fgsea() test suite with the enrichit GSEA leading-edge contract written for YuLab-SMU/DOSE#46:
    • The rank-vector assertions in tests/testthat/test-converters.R now check, in order: expect_type(result$rank, "integer"), expect_false(anyNA(result$rank)), expect_true(all(rank >= 0L)).
    • The final check carries an in-line comment documenting the canonical rank == 0L no-signal sentinel — "no usable weighted in-set signal for this pathway" (N_R == 0, empty gene-set overlap, or a non-finite running score; matches enrichit >= 0.2.5.9008).
    • Together the three assertions guard against silent type drift (numeric 0 or NA_real_ leaking in for the documented integer sentinel) and against accidental re-introduction of an NA_integer_ sentinel that would collapse all(c(NA, 4) >= 0L) to NA instead of a clean boolean. (2026-10-05, Mon, TRAE Code Review closes issue I1; aligns with YuLab-SMU/enrichit >= 0.2.5.9008)

enrichplot 1.99.7

  • add opt-in threshold, top_k and adaptive edge filters to emapplot() and ssplot(); top_k keeps strongest per-term neighbors, while adaptive targets a configurable graph density without changing the similarity matrix or dimension-reduction input (2026-09-27, Sun)
  • expose min_edge and size_edge directly in ssplot(), document classical MDS as one available reduction choice, and add an optional enrichplot_edge_diagnostic attribute plus emapplot_edge_density() helper for retained-pair density diagnostics (2026-09-27, Sun)
  • harden similarity-space selection for term IDs, preserve labels through one- and two-term reductions, and validate edge/coordinate controls before plotting (2026-09-27, Sun)

enrichplot 1.99.6

  • fix hplot() visual semantics by replacing the inaccurate ribbon/rug approximation with a pure ggplot2 horizon-band implementation: four BluGrn score bands, minimum-origin scaling, stacked facet geometry and right-side term labels now match the historical ggHoriPlot::geom_horizon(origin = "min", horizonscale = 4) output without requiring ggHoriPlot (2026-09-24, Thu)

  • fix cnetplot() S3 generic/method consistency under R CMD check: the enrichResult, gseaResult and compareClusterResult methods now match the current ggtangle::cnetplot() signature while retaining legacy controls such as categorySize, circular, colorEdge, pie, split and includeAll through ... (2026-09-24, Thu)

  • fix treeplot(cluster_panel = "dotplot") with current ggtreeExtra: the fruit layer now uses the geometry name and mappings expected by ggtreeExtra, and the method works when ggplot2 is not attached (2026-09-24, Thu)

  • fix hplot() failures when ggplot2 is not attached: expansion() is now called through the ggplot2 namespace (2026-09-24, Thu)

  • make external-result importers citation-neutral: import_enrichr(), import_gprofiler2(), import_webgestalt() and import_fgsea() now display imported-result summaries without claiming a clusterProfiler citation, and use supplied adjusted p-values or deterministic p-adjusted fallbacks for small tables (2026-09-24, Thu)

  • fix package checks for test fixtures by declaring the Matrix package used in mnsea mock results, and add regression coverage for the repaired plotting paths (2026-09-24, Thu)

  • treeplot(), emapplot() and ssplot() now explain a missing term-similarity matrix instead of failing with no 'dimnames' attribute for array: when pairwise_termsim() has not been run, the error now says so and shows the call to make. The existing has_pairsim() guard had been left unwired, so the cryptic crash was what users actually saw (2026-09-22, Tue)

  • cnetplot() now warns when none of the names in foldChange match the genes of the result (#177): the item nodes are drawn grey in that case, which is easily misread as "foldChange was ignored", so the mismatch is reported along with the expected ID style (2026-09-22, Tue)

  • fix cnetplot() categorySizeBy formulas for compareClusterResult: the legacy-argument shim forces the argument before it is captured, which left the quosure's environment empty, so every formula failed at draw time with could not find function "-"; the expression is now evaluated in the formula's own environment, so categorySizeBy = ~-log10(p.adjust) works again (2026-09-22, Tue)

  • fix cnetplot() legacy circular, edge-color, and category-size arguments (#330): the wrapper now translates circular = TRUE to the current circular layout, colorEdge = TRUE to category-colored edges, and legacy categorySize strings to the current categorySizeBy semantics, so older fold-change cnetplot calls build again without leaking stale arguments into the layout backend (2026-09-22, Tue)

  • fix dotplot() p-value color legend labels for very small values (#277): p-value / p-adjusted / q-value breaks below 1e-3 are now shown in readable scientific notation instead of long unreadable decimals (2026-09-22, Tue)

  • document dotplot() size behavior for gseaResult (#206): when x is "GeneRatio" the point size defaults to "count" (number of genes); size = "GeneRatio" scales it by the enrichment gene ratio instead (2026-09-22, Tue)

  • fix ridgeplot() for mnseaResult with small per-feature contributions: the undersized-gene-set guard (intended for gseaResult density estimation) no longer drops mnsea mechanism groups that only carry a few feature scores, so layered mnsea ridgeplots render again instead of aborting (2026-09-22, Tue)

  • gseaplot2(): pvalue_table now defaults to NES and p.adjust columns instead of two redundant p-value columns; columns remain fully configurable via pvalue_table_columns and row names can be suppressed with pvalue_table_rownames = NULL (2026-09-22, Tue)

  • cnetplot() supports node_label_size (#41): control the font size of the category/item node labels; defaults to the built-in size when NULL (backed by the same parameter in ggtangle)

  • guard cnetplot() compare-cluster pies across showCategory sizes (#284): add a regression test that exercises pie = "count" while increasing showCategory, ensuring term nodes expand consistently and both plots still build cleanly (2026-09-22, Tue)

  • guard treeplot() against tidytree helper renames (#249, #247): add a regression test that explicitly exercises the current tidytree namespace shape (private .offspring.tbl_tree_item without exported offspring.tbl_tree_item) while ensuring treeplot() still builds cleanly (2026-09-22, Tue)

enrichplot 1.99.5

  • guard dotplot() compare-cluster labels against geneRatio regressions (#180): add a regression test that keeps by = "geneRatio" and by = "count" from reintroducing NA cluster labels in compare-cluster dotplots (2026-09-22, Tue)
  • fix treeplot() split-aware faceting for GSEA results (#169): split is now carried into tree, tip, and clade metadata so treeplot(..., split = ".sign") + facet_grid(. ~ .sign) builds instead of dropping the faceting variable from every layer (2026-09-22, Tue)
  • fix treeplot() cluster color assignment when nCluster reaches two digits (#171): cluster palettes and clade-label groups now follow numeric cluster ids instead of lexical ordering, so groups like cluster_10 no longer steal cluster_2 colors when the cluster count increases (2026-09-22, Tue)
  • fix emapplot() compare-cluster pie nodes across ontologies (#228): ontology-specific terms that share the same Description now keep stable ID-backed labels all the way into pie-layer data alignment, so compareCluster(..., ont = "ALL") no longer collapses those nodes or breaks while building the pie overlay (2026-09-22, Tue)

enrichplot 1.99.4

  • fix goplot() DAG construction for top-level GO terms: parent edges that point to the synthetic all root are now dropped before the graph is built, so plots that include terms such as GO:0008150 no longer fail with Some vertex names in \d` are not listed in `vertices`` (2026-09-22, Tue)
  • fix heatplot() dot-mode p-value scaling: zero or non-positive gene p-values are now clamped to the smallest positive double before the reversed log-size transform is applied, so significance-sized dots no longer emit infinite-value warnings for exact-zero inputs (2026-09-22, Tue)
  • fix ridgeplot() blank rows for undersized core gene sets (#288): pathways with fewer than three ranked values are now dropped before geom_density_ridges() is built, and the function now errors clearly when no selected pathway has enough values to estimate a density, so two-gene core sets no longer leave empty y-axis slots in the plot (2026-09-21, Mon)

enrichplot 1.99.3

  • fix cnetplot() for compareClusterResult terms with duplicated descriptions (#279): category nodes now use stable ID-backed labels internally, so distinct terms that share the same Description are no longer merged into one network node, with regression coverage for the duplicated-label case (2026-09-21, Mon)
  • fix treeplot() heatmap panels for compareClusterResult: the cluster_panel = "heatMap" path now calls ggtree::gheatmap() with the active tree plot object instead of treating it like a regular layer, so compare-cluster treeplots render again instead of failing with a missing data argument error (2026-09-21, Mon)
  • fix treeplot() dotplot panels for compareClusterResult (#232, #224): the cluster_panel = "dotplot" path now passes ggtreeExtra::geom_fruit() the plain term columns it expects, so compare-cluster treeplots render again on current ggtreeExtra builds instead of failing while decoding the y mapping (2026-09-21, Mon)

enrichplot 1.99.2

  • support importing results from external enrichment tools: import_enrichr(), import_gprofiler2(), import_webgestalt() and import_fgsea() map enrichr / g:Profiler / WebGestaltR / fgsea output tables to enrichResult / gseaResult objects that plug into the 'enrichplot' visualization functions; the 'enrichit' constructors as_enrichResult() / as_gseaResult() are re-exported for other table formats (2026-09-21, Mon)
  • fix dotplot() legend keys under plot composition (#273): size legends now keep the hollow point shape after cowplot::plot_grid() / similar grob composition, instead of reverting to solid circles in combined figures (2026-09-21, Mon)
  • fix dotplot() size scaling for enrichment results (#118): size = "Percentage" now derives a percentage column from GeneRatio for enrichResult / gseaResult data instead of failing at draw time with a missing-column error (2026-09-21, Mon)
  • fix barplot() width handling (#201): width = ... is now forwarded to the internal geom_col() layer for both enrichment-result and compare-cluster barplots, so bar thickness can be adjusted directly without stacking a second geom_col() layer on top of the original bars (2026-09-21, Mon)
  • fix dotplot() selection ordering for numeric showCategory (#345, #219): the function now orders the fortified data by orderBy first and only then takes the requested top rows, so the leading categories stay stable when showCategory changes and orderBy is honored correctly (2026-09-21, Mon)

enrichplot 1.99.1

  • fix upsetplot() for readable gseaResult objects (#179): the fold-change vector is now remapped through fc_readable(), so setReadable() results no longer lose all ranked-score values when pathway genes are shown as symbols (2026-09-21, Mon)
  • improve gseaplot() / gseaplot2() multi-panel compatibility with cowplot (#239): the gglist-level cowplot::as_grob() bridge is now implemented in aplot, so plot_grid() / ggarrange() work when paired with an aplot version that provides that helper, without making it a hard requirement for enrichplot itself (2026-09-21, Mon)
  • fix upsetplot() boxplot overlays for gseaResult and mnseaResult (#178): the boxplot layer now suppresses its own outlier glyphs so jittered feature points are drawn only once instead of being duplicated on top of boxplot outliers (2026-09-21, Mon)
  • fix pairwise_termsim() for enrichResult objects whose raw result table has terms but the object cutoffs filter them all out of as.data.frame() (#269): term selection now uses the raw result rows, so showCategory can still pick the requested top terms and downstream plots such as emapplot() continue to work for non-significant result tables (2026-09-21, Mon)
  • fix grouped emapplot() / ssplot() legend control (#292): the compatibility arguments group and group_legend are accepted again, and grouped layouts no longer force the "groups" legend on when group_legend = FALSE is requested (2026-09-21, Mon)
  • fix gseaplot2() hit-bin rectangles for single gene sets (#221, #20): the colored bins under the hit ticks now follow the ranked-list direction instead of mirroring the cumulative hit counts, so highly one-sided enrichments no longer collapse the wide interval onto the wrong end of the plot (2026-09-21, Mon)
  • fix cnetplot() / emapplot() for compareClusterResult pie nodes when duplicated (Cluster, Description) rows are present (#314): pie counts are now aggregated before widening, avoiding list-columns and the tidyr cast error ("Can't convert fill to "), with regression coverage for duplicated cluster-term inputs (2026-09-21, Mon)
  • fix barplot() for compareClusterResult objects: the default by = "geneRatio" and by = "rowPercentage" crashed in plotting.clusterProfile(), and by = "count" failed at rendering time under ggplot2 4.x; by is now mapped to the fortify-produced column and bars are drawn with geom_col() (2026-09-21, Mon)
  • fix emapplot() / ssplot() with similarity measures other than 'JC' (e.g., 'Wang') (#309): label-keyed similarity matrices were re-mapped as term IDs, producing NA edges ("edge data frame contains NAs"); the stale re-mapping in build_emap_graph() was removed (2026-09-21, Mon)
  • add a plotting regression suite (test-plotting-regression.R) covering the tutorial-facing visualization functions, including a dispatch canary for the ggplot() + theme_dose() failure seen under ggplot2 4.0.x with S7 < 0.2.2; ggplot outputs are evaluated with ggplot_build() to catch bad aesthetics (2026-09-21, Mon)

enrichplot 1.33.1

  • complete remaining mechanism-plot enhancements: pairwise_termsim() now supports layer-aware similarity for mnseaResult, classification thresholds are exposed through phaseplot() / consensusmap() / mechanismflow(), and an explicit nseaResult mock plus coverage has been added for nsea plotting paths; gsInfo.gseaResult() also defaults exponent to 1 when params lacks it (2026-08-29, Sun)
  • refactor gsInfo() into an S3 generic and add layer-aware running-score support to gseaplot2(), gsearank() and hplot() for nseaResult / mnseaResult; hplot() is now implemented with base ggplot2 geoms and no longer requires ggHoriPlot (2026-08-23, Sun)
  • add pairwise_termsim() support for mnseaResult so treeplot(), emapplot() and ssplot() share one layer-aware similarity definition, with single-pathway treeplot boundary handling
  • add barplot.gseaResult() so nseaResult / mnseaResult no longer fall through to graphics::barplot.default
  • add mechanism-oriented helper layer (compute_rewiring_score(), classify_mechanism_state(), summarize_nsea_mechanism(), extract_rewiring_features()) with deterministic tests
  • add phaseplot() for enrichment-shift versus rewiring overviews and rewireplot() for pathway-specific feature-level rewiring evidence
  • add consensusmap() for multi-context mechanism agreement and mechanismflow() for pathway state transitions across layers/conditions
  • refine mechanism plots with real cross-object comparisons: summarize_nsea_mechanism() now accepts a reference result to compute delta_NES and cross-object rewiring_score; phaseplot() supports reference / x_axis / size_var; consensusmap() uses fill for NES/delta NES and point size for rewiring/overlap; mechanismflow() uses flow magnitude and stable mechanism-state ordering (2026-08-23, Sun)
  • add a minimal ssplot.mnseaResult() that projects selected pathways into a similarity-space overview using layer-aware feature overlap, while reusing emapplot() semantics and adding stable fallbacks for one- or two-pathway layouts (2026-06-25, Thu)
  • add a minimal upsetplot.mnseaResult() that summarizes shared feature overlaps across selected pathways with collapsed-score or single-layer views, including support for score magnitude display and core_enrichment filtering (2026-06-25, Thu)
  • add a minimal ridgeplot.mnseaResult() that shows pathway-level feature score distributions from collapsed scores or a selected single layer, with regression coverage for layer-aware ranked scores and core_enrichment filtering (2026-06-25, Thu)
  • add a minimal gseaplot.mnseaResult() that supports collapsed-score and single-layer running-score views for one pathway at a time, with regression coverage for stable pathway selection and layer-aware ranked scores (2026-06-25, Thu)
  • batch-refine mnsea plot semantics by aligning layer filtering and readable legend labels across dotplot(), heatplot(), cnetplot() and emapplot(), while fixing emapplot.mnseaResult() to retain all selected pathways when rebuilding overlap graphs after layer filtering, with expanded regression coverage (2026-06-25, Thu)
  • add a minimal emapplot.mnseaResult() that reuses cached term similarity when available and otherwise falls back to internal JC overlap for pathway-level map plots, with regression coverage (2026-06-24, Wed)
  • batch-refine cnetplot.mnseaResult() readability by splitting pathway and feature label layers, preferring shared features when labels are capped, and stabilizing layer ordering with expanded regression coverage (2026-06-24, Wed)
  • refine default label selection in cnetplot.mnseaResult() to keep pathway annotations while deduplicating repeated feature labels across layers, with regression coverage for the quieter defaults (2026-06-24, Wed)
  • clarify cnetplot.mnseaResult() legend titles for edge type, node type, layer, feature sign, and feature magnitude, with regression coverage for the updated defaults (2026-06-24, Wed)
  • distinguish pathway and feature nodes in cnetplot.mnseaResult() with explicit node-type shapes and regression coverage for the updated legend semantics (2026-06-24, Wed)
  • refine cnetplot.mnseaResult() with edge-type legends, effective size_edge scaling, and feature-node sign encoding backed by lightweight regression tests (2026-06-24, Wed)
  • align default pathway_id resolution across mnsea helpers and feature-level heatplot(), and add share / exclusive label support to cnetplot.mnseaResult() with regression coverage (2026-06-24, Wed)
  • add cnetplot.mnseaResult() for pathway-specific multilayer subnetworks, including pathway anchor nodes and lightweight regression coverage for the new network view (2026-06-24, Wed)
  • add heatplot.mnseaResult() for term-layer and pathway-specific feature heatmaps, and cover the new mnsea helper/plotting workflow with lightweight tests (2026-06-24, Wed)
  • refactor shared plot data preparation for cnetplot(), emapplot(), heatplot() and pairwise_termsim() around unified term selection helpers, and add smoke tests for compareClusterResult network visualizations (2026-06-24, Wed)
  • add a minimal testthat skeleton for regression coverage, and align update_n() / pairwise_termsim() / get_similarity_matrix() with stable term selection semantics (2026-06-24, Wed)
  • fix heatplot(showTop) to fail early when foldChange is missing, correct the reverse behavior in set_enrichplot_color(), and add runtime checks for optional plotting dependencies (2026-06-24, Wed)
  • harden term selection and label handling across cnetplot(), emapplot(), pairwise_termsim() and upsetplot() by using stable term identifiers internally while keeping display labels readable (2026-06-24, Wed)

enrichplot 1.32.0

  • Bioconductor RELEASE_3_23 (2026-04-29, Wed)

enrichplot 1.31.5

  • cnetplot.compareClusterResult() now supports categorySizeBy for category pie sizing and aligns docs with ggtangle::cnetplot() semantics (2026-04-22, Wed)
  • ridgeplot now supports stat parameter (default is 'density_ridges' and can be changed to 'binline') (2026-04-01, Wed, #343)
  • manhattan plot for enriched result (2026-03-26, Thu)
  • update roxygen document to use markdown syntax (2026-03-02, Mon)
  • bug fixed in xy-lab format in ssplot() (2026-03-02, Mon)
  • bug fixed in formula supports in dotplot() (2026-02-26, Thu)

enrichplot 1.31.4

  • fix cnetplot() S3 generic/method consistency warnings (2026-01-14, Wed)
  • fix treeplot() column selection bug when color variable equals size variable (2026-01-14, Wed)
  • fix fortify.compareClusterResult() warnings about missing imports and global variables (2026-01-14, Wed)
  • remove plyr and use dplyr in method-fortify.R (2026-01-14, Wed)
  • fixed treeplot() issue where pairwise_termsim() with method="JC" produced unnamed similarity matrix, causing "undefined column selected" error (2025-01-14)
  • fixed fortify.compareClusterResult() warning "NAs introduced by coercion" when Cluster names are not numeric (2025-01-14)
  • bug fixed in barplot() as fortify() generic in ggplot2 checks for unused arguments in ... (2026-01-14, Wed)
  • remove categorySize parameter in cnetplot() (2026-01-14, Wed)
  • bug fixed in goplot() as GOSemSim uses cache (2026-01-13, Tue)
    • also fix gotbl object not found issue (2026-01-13, Tue)
  • re-export geneID, geneInCategory and gseaScores from 'enrichit' (2026-01-12, Mon)
  • update documentation: fix typos, grammar errors and use modern markdown syntax (2026-01-12, Mon)
  • bug fixed in update_n() if showCategory is a vector of term names (2026-01-08, Thu)
  • avoid the "condition has length > 1" error in outer() by using Vectorize() (2026-01-08, Thu)

enrichplot 1.31.3

  • use 'enrichit' package (2025-12-07, Sun)
  • optimize source code (2025-12-02, Tue)
  • error handling functions imported from 'yulab.utils' (2025-12-01, Mon)

enrichplot 1.31.2

  • add 'fc_threshold' parameter to cnetplot (2025-11-30, Sun, #338)
    • requires 'ggtangle' v>= 0.0.9
  • update all line width aes mapping from 'size' to 'linewidth' (2025-11-30, Sun)
  • add 'node_label_size' parameter for emapplot (2025-11-30, Sun)
  • remove emapplot parameters, 'group', 'group_style' and 'label_group_style' (#339)
  • add 'showTop' parameter to limit number of genes shown in heatplot() and distinguish tip point size variable for treeplot() through internal parameter size_var (2025-11-23, Sat, #335)

enrichplot 1.31.1

  • import ggfun::%<+% (2025-11-18, Tue)
  • update ssplot(), treeplot() and get_wordcloud() (2025-11-15, Sat)
  • change set_enrichplot_color(transform = 'identity') as default behavior (2025-11-11, Tue)
    • now it only sets the color scale without changing the transform method
    • explicitly set transform = 'log10' in dotplot
  • use 'quarto' as vignette engine (2025-11-11, Tue)
  • use set_enrichplot_color(transform = 'identity') in heatplot (2025-11-11, Tue)
  • use set_enrichplot_color(transform = 'identity') in cnetplot (2025-11-05, Wed)

enrichplot 1.30.0

  • Bioconductor RELEASE_3_22 (2025-11-01, Sat)

enrichplot 1.29.4

  • remove deprecated aes_string/aes_ (2025-10-23, Thu, #332)

enrichplot 1.29.3

  • bug fixed of cnetplot for CompareClusterResult (2025-09-13, Sat, #329)
    • color gene according to the gene cluster info
  • bug fixed in pie scale label (2025-07-14, Mon, #328)

enrichplot 1.29.2

  • update treeplot with two parameters, leave_fontsize and clade_fontsize (2025-07-12, Sat, #324, #325)
    • remove the fontsize parameter as it only works for clade_fontsize
  • 'log10' transform for pvalue color scale by default (2025-07-12, Sat, #316)
  • introduce new parameters in gseaplot2() (2025-07-12, Sat)

enrichplot 1.29.1

  • throw error in goplot() if ontology is not one of the 'MF', 'CC' or 'BP' (2025-04-28, Mon, clusterProfiler#768)

enrichplot 1.28.0

  • Bioconductor RELEASE_3_21 (2025-04-17, Thu)

enrichplot 1.27.5

  • able to scale pie size for 'compareClusterResult' (2025-03-11, Tue, #308, #311)

enrichplot 1.27.4

  • adjust pie size and category label position in cnetplot() (2025-01-08, Wed, #306)
  • clean up code (2024-12-20, Fri)

enrichplot 1.27.3

  • scale pies and add pie legend in emapplot() (2024-12-12, Thu, #304)
  • a safe way to extract gene sets in ridgeplot() (2024-12-12, Thu, #303)

enrichplot 1.27.2

  • emapplot() now allows passing color to a specific color, e.g., color = "black" (2024-11-29, Fri, #300)
  • bug fixed in emapplot()
    • size_category now works for pie node (2024-11-29, Fri, #301)
    • legend of term nodes will be retained when group = TRUE (2024-11-29, Fri, #300)
  • supports passing ID to 'showCategory' in ridgeplot() (2024-11-06, Wed, #295)
  • enhancement of cnetplot() (2024-11-06, Wed)
    • 'node_label' can be a vector of selected items/genes to specify the items to be displayed (#293)
    • 'node_label' can be 'exclusive' to label genes that are uniquely belongs to categories (#253)
    • 'node_label' can be 'share' to label genes that are share between categories (#253)
    • 'node_label' can be, e.g. '> 1' or '< 1', to label genes that have log2FC values larger or smaller than the threshold (#253)
    • supports using ggtangle::geom_cnet_label() to label items/genes in independent layer (#194, #266, #267)
  • fixed ridgeplot() when selecting a specific gene set and plotting non-core genes (2024-11-06, Wed, #298)

enrichplot 1.27.1

enrichplot 1.26.0

  • Bioconductor RELEASE_3_20 (2024-10-30, Wed)

enrichplot 1.25.6

  • pretty gene count legend (2024-10-29, Tue, #271)

enrichplot 1.25.5

  • new emaplot(), goplot(), cnetplot() and ssplot(), all power by 'ggtangle' package (2024-10-24, Thu)
  • re-export ggtangle::cnetplot() (2024-10-24, Thu)
  • remove drag_network() (2024-10-24, Thu)

enrichplot 1.25.4

  • fixed goplot() (2024-10-23, Wed, #297, #732, #718)

enrichplot 1.25.3

  • hplot(): Horizontal plot for GSEA result (2024-08-27, Tue)

enrichplot 1.25.2

  • fixed bug in ridgeplot() (2024-08-19, Mon, clusterProfiler#704)

enrichplot 1.25.1

  • fixed GeneRatio in dotplot as character of fraction issue (2024-08-16, Fri, clusterProfiler#715)
  • use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)
  • dotplot2 to compare two selected clusters in 'compareClusterResult' object (2024-06-15, Sat)
  • volplot to visualize ORA result using volcano plot (2024-06-13, Thu)

enrichplot 1.24.0

  • Bioconductor RELEASE_3_19 (2024-05-15, Wed)

enrichplot 1.23.2

  • separate the JC similarity method (2023-12-11, Mon, #265)
  • fix the issue in ridgeplot(showCategory) : support a vector of Description, not ID(2023-12-1, Fri, #193)

enrichplot 1.23.1

  • ridgeplot() supports passing a vector of selected pathways via the 'showCategory' parameter (2023-11-30, Thu, #193)
  • fix treeplot() to compatible with the current version of ggtree and ggtreeExtra. (2023-10-28, Sat)
  • add clusterPanel.params[["colnames_angle"]] parameter to set the angle of colnames. (2023-10-28, Sat)

enrichplot 1.22.0

  • Bioconductor RELEASE_3_18 (2023-10-25, Wed)

enrichplot 1.21.3

  • set_enrichplot_color(), a helper function to set colors (2023-09-13, Wed)
    • change default color: from c("red", "blue") to c("#e06663", "#327eba")
  • use check_installed() to check package dependency (2023-09-08, Fri, #254)

enrichplot 1.21.2

  • introduce 'facet' parameter in dotplot() method for compareClusterResult. If facet = "intersect", the dots will be separated by enriched pathway intersection among clusters. It can set to other variable that can be used for splitting the figure (e.g., "category" for KEGG results) (2023-08-21, Mon)

enrichplot 1.21.1

  • fixed cnetplot.compareClusterResult() for only contains one cluster (2023-05-24, Wed, #243)

enrichplot 1.20.0

  • Bioconductor RELEASE_3_17 (2023-05-03, Wed)

enrichplot 1.19.2

  • fix emapplot() for parameter mismatch (2023-02-20, Mon)
  • fix ridgeplot for error when x@readable == TRUE and length(x@gene2Symbol) = 0 (2022-12-5, Mon)
  • fix ridgeplot for error when x@readable == TRUE and length(x@gene2Symbol) = 0 (2022-12-5, Mon, #217)

enrichplot 1.19.1

  • fix cnetplot() for node_label parameter is flipped(2022-12-04, Sun, #216)
  • bug fixed in treeplot() (2022-11-18, Fri)
  • enable dotplot() and autofacet() for gseaResultList object

enrichplot 1.18.0

  • Bioconductor RELEASE_3_16 (2022-11-02, Wed)

enrichplot 1.17.4

  • rename parameters of emapplot(), centplot() and treeplot() (2022-09-11, Sun)

enrichplot 1.17.3

  • align the dots in treeplot() (2022-10-1, Sat)
  • fix a bug in color legend of treeplot() (2022-10-1, Sat)

enrichplot 1.17.2

  • autofacet to automatically split barplot and dotplot into several facets (2022-09-06, Tue)
  • dotplot method for enrichResultList object
  • add parameters hilight_category, alpha_hilight, alpha_nohilight for cnetplot() and emapplot (2022-09-4, Sun)
  • change round digits of cnetplot scatterpie legend to 1 (2022_8_29, Mon).
  • gsearank() can export result as a table when output = "table" (2022-08-29, Mon, #184)
  • fix a bug in fc_readable() (2022-08-29, Mon, #189)
  • allows passing color="NES" to dotplot() for gseaResult object (2022-08-29, Mon, #14)

enrichplot 1.17.1

  • fix a bug in YuLab-SMU/clusterProfiler#488 (2022-08-25, Thu)
  • support multiple gene sets in geom_gsea_gene layer (2022-08-25, Thu)
  • geom_gsea_gene layer (2022-08-24, Wed)
  • add parameters symbol and pvalue for heatplot.enrichResult() (2022-08-20, Sat)
  • change default values of group_category and node_label in ssplot() (2022-07-04, Mon)
  • update document of ssplot() (2022-07-04, Mon)
  • gseaplot() and gseaplot2() return gglist object instead of plotting the figure (2022-05-05, Thu)
  • fix ridgeplot when x@readable = TRUE (2022-04-30, Sat)

enrichplot 1.16.0

  • Bioconductor 3.15 release

enrichplot 1.15.4

  • update treeplot: support passing rel object to offset and offset_tiplab (2022-04-24, Sun)

enrichplot 1.15.3

  • export `drag_network' (2022-03-07, Mon)
  • update cnetplot.enrichResult to be supported by drag_network(2022-3-6, Sun)
  • add function drag_network to drag the nodes of networks (2022-2-25, Fri)
  • fix a bug in goplot: goplot.gseaResult need setType slot instead of ontology slot (2022-2-22, Tue)
  • return gg object instead of print it in dotplot.compareClusterResult() (2022-01-05, Wed, @altairwei, #160)

enrichplot 1.15.2

  • add label_format_tiplab and label_format_cladelab parameters for treeplot(2021-12-24, Fri)
  • support treeplot of compareCluster(GSEA algorithm) result(2021-12-13, Mon)
  • support visualization of compareCluster(GSEA algorithm) result(2021-12-11, Sat)
  • support scientific notation for gseaplot2(2021-12-4, Sat)

enrichplot 1.15.1

  • fixed R check by importing utils

enrichplot 1.14.0

  • Bioconductor 3.14 release

enrichplot 1.13.2

  • mv ep_str_wrap to yulab.utils::str_wrap (2021-10-13, Wed)
  • adjust the order of legends for dotplot, emapplot, cnetplot and treeplot(2021-10-8, Fri)
  • update treeplot: add "dotplot" and "heatmap" panels for treeplot(2021-9-15, Wed)
  • update dotplot: enable size parameter applicable to other columns of compareClusterResult(2021-9-17, Fri)
  • enable label_format parameter for heatplot (2021-09-01, Wed)
  • add get_ggrepel_segsize function to set segment.size value for ggrepel(2021-08-29, Sun)
  • update ep_str_wrap (2021-08-28, Sat)
  • cnetplot now works with a named list (2021-08-23, Mon; clusterProfiler#362)

enrichplot 1.13.1

  • use aplot::plot_list instead of cowplot::plot_grid (2021-06-13, Sun
  • add color_category and color_gene parameters for cnetplot(2021-6-11, Fri)
  • Enables showCategory parameter to support character input in dotplot.compareClusterResult(2021-6-10, Thu)

enrichplot 1.12.0

  • Bioconductor 3.13 release

enrichplot 1.11.3

  • add function ssplot for similarity space plot. (2021-4-22, Thu).
  • Reconstruct the emapplot function and replace emapplot_cluster by emapplot(group_category = TRUE)
  • fix bug in emapplot_cluster.enrichResult when the number of cluster is 2 (2021-2-24, Wed).
  • fix bug in treeplot: The legend is not the right size (2021-2-6, Sat).
  • fix dotplot for label_format parameter doesn't work(2021-2-3, Wed).
  • fix bug in gseaplot2(2021-1-28, Thu)

enrichplot 1.11.2

  • update document (2021-1-7, Thu)
  • update dotplot: replace ggsymbol::geom_symbol with ggstar::geom_star(2021-1-6, Wed)
  • add parameter shadowtext for three functions: emapplot, emapplot_cluster and cnetplot. (2021-1-5, Tue)
  • update dotplot: supports the use of shapes and line colors to distinguish groups (2021-1-3, Sun)
  • add treeplot function (2020-12-29, Tue)
  • rename function get_ww to get_similarity_matrix (2020-12-29, Tue)
  • move the emapplot related functions to emapplot_utilities.R
  • fix bug in emapplot and cnetplot when enrichment result is one line (2020-12-26, Sat)
  • fix pairwise_termsim for the bug of repeated filtering of showCategory(2020-12-23, Wed)
  • fix showCategory for cnetplot, emapplot, emapplot_cluster when showCategory is a vector of term descriptions

enrichplot 1.11.1

  • add orderBy and decreasing parameters for ridgeplot() (2020-11-19, Thu)
  • update emapplot_cluster() to label cluster in center by default and use ggrepel if setting repel = TRUE (2020-11-08, Mon)
  • add a label_format parameter to support formatting label (2020-10-28, Wed)
    • if provided with a numeric value will simply string wrap by default
    • if provided with a function will instead set labels = user_defined_function() within the scale function
    • #73

enrichplot 1.10.0

  • Bioconductor 3.12 release (2020-10-28, Wed)

enrichplot 1.9.5

  • fix wordcloud_i (2020-10-15, Thu)
  • Remove similarity calculation from emapplot

enrichplot 1.9.4

  • implement pairwise_termsim to calculate similarity of enriched terms (2020-10-09, Fri)
  • change parameters to be more consistent

enrichplot 1.9.3

  • add node_label_size parameter to adjust the size of node label in emapplot function (2020-09-18, Fri)

enrichplot 1.9.2

  • add function emapplot_cluster (2020-09-01, Tue)

enrichplot 1.7.3

  • update barplot to remove using coord_flip() (2020-09-10, Thu)
  • update cnetplot color scale to tolerate with skewed foldchange (2020-03-13, Fri)

enrichplot 1.7.1

  • cnetplot for compareClusterResult (compareCluster output) (2019-12-02, Mon)
  • move barplot, dotplot and fortify methods of compareClusterResult from clusterProfiler (2019-11-2, Sat)

enrichplot 1.6.0

  • Bioconductor 3.10 release

enrichplot 1.5.2

enrichplot 1.5.1

  • gseadist for plotting logFC distribution of selected gene sets. (2019-06-25, Tue)

enrichplot 1.4.0

  • Bioconductor 3.9 release

enrichplot 1.3.2

  • dotplot supports setting x to other variable, e.g. NES (2019-01-10, Thu)
  • mv vignette to clusterProfiler-book.

enrichplot 1.2.0

  • Bioconductor 3.8 release

enrichplot 1.1.5

  • gsearank for plotting ranked list of genes belong to specific gene set (2018-07-04, Wed)

enrichplot 1.1.4

  • base_size parameter in gseaplot2 (2018-06-21, Thu)

enrichplot 1.1.3

  • pmcplot for plotting pubmed trend (2018-06-14, Thu)
  • ggtable for plotting table
  • gseaplot2 now accepts a vector of geneSetID (2018-06-13, Wed)

enrichplot 1.1.2

  • emapplot supports showCategory parameter to accept a vector of Description (2018-05-29, Tue)
  • bug fixed of showCategory parameter for vector of Description in cnetplot
  • gseaplot2 that mimic the figure generated by broad institute's GSEA software (2018-05-28, Mon)

enrichplot 1.1.1

enrichplot 1.0.0

  • Bioconductor 3.7 release

enrichplot 0.99.14

enrichplot 0.99.13

  • fixed goplot issue by imporint ggraph <2018-03-12, Mon>

    • #5

    • Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), :

    invalid line type

  • dotplot now supports orderBy and decreasing parameters to specify the order of dots by order(x[[orderBy]], decreasing=decreasing)

enrichplot 0.99.9

  • defined upsetplot (2018-01-30, Tue)
  • all visualization methods were defined as S4 methods (2018-01-29, Mon)

enrichplot 0.99.5

  • defined all visualization functions as generic functions (2018-01-03, Wed)
  • add colorEdge parameter in cnetplot
  • update docs

enrichplot 0.99.3

  • import ggplot2::rel to fix R check (2017-11-28, Tue)

enrichplot 0.99.0

  • ready to submit to Bioconductor (2017-11-28, Tue)

enrichplot 0.0.3

  • heatplot and gseaplot (2017-11-28, Tue)
  • ridgeplot, barplot and dotplot derived from DOSE (2017-11-28, Tue)
  • cnetplot (2017-11-28, Tue)

enrichplot 0.0.2

  • vignette added (2017-11-28, Tue)
  • goplot for plotting induced GO DAG (2017-11-27, Mon)

enrichplot 0.0.1

  • emapplot for plotting enrichment map (2017-11-23)