emapplot() / ssplot() no longer require the suggested ggforce package,
and the grouping controls are consolidated on node_label:
ggforce is not installed the group outline falls back to
ggplot2::stat_ellipse(). Grouping is on by default in ssplot(), so the
previous unconditional check_installed("ggforce") made the default call
abort on a machine without a merely suggested package.node_label = "category_grouped" replaces group = TRUE (outline the
groups, label the categories); group = FALSE is node_label = "none".
group still works but now warns as deprecated.node_label is an error instead of silently drawing nothing,
and a non-default top_k / target_density that the selected
edge_filter does not use warns instead of being dropped silently.emapplot() itself, so "all"
labels the groups exactly as "group" does, and the node_label values
together with their outlines and labels are tabulated in ?emapplot and
?ssplot.
(2026-10-09, Fri)import_fgsea() test suite with the enrichit GSEA leading-edge
contract written for YuLab-SMU/DOSE#46:
tests/testthat/test-converters.R now
check, in order: expect_type(result$rank, "integer"),
expect_false(anyNA(result$rank)), expect_true(all(rank >= 0L)).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).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, aligns with
YuLab-SMU/enrichit >= 0.2.6)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)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)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)
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)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)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)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)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)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)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)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)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)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)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)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)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)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)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)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)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)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)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)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)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)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 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)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)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)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)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)pairwise_termsim() support for mnseaResult so treeplot(), emapplot() and ssplot() share one layer-aware similarity definition, with single-pathway treeplot boundary handlingbarplot.gseaResult() so nseaResult / mnseaResult no longer fall through to graphics::barplot.defaultcompute_rewiring_score(), classify_mechanism_state(), summarize_nsea_mechanism(), extract_rewiring_features()) with deterministic testsphaseplot() for enrichment-shift versus rewiring overviews and rewireplot() for pathway-specific feature-level rewiring evidenceconsensusmap() for multi-context mechanism agreement and mechanismflow() for pathway state transitions across layers/conditionssummarize_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)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)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)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)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)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)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)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)cnetplot.mnseaResult() to keep pathway annotations while deduplicating repeated feature labels across layers, with regression coverage for the quieter defaults (2026-06-24, Wed)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)cnetplot.mnseaResult() with explicit node-type shapes and regression coverage for the updated legend semantics (2026-06-24, Wed)cnetplot.mnseaResult() with edge-type legends, effective size_edge scaling, and feature-node sign encoding backed by lightweight regression tests (2026-06-24, Wed)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)cnetplot.mnseaResult() for pathway-specific multilayer subnetworks, including pathway anchor nodes and lightweight regression coverage for the new network view (2026-06-24, Wed)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)cnetplot(), emapplot(), heatplot() and pairwise_termsim() around unified term selection helpers, and add smoke tests for compareClusterResult network visualizations (2026-06-24, Wed)testthat skeleton for regression coverage, and align update_n() / pairwise_termsim() / get_similarity_matrix() with stable term selection semantics (2026-06-24, Wed)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)cnetplot(), emapplot(), pairwise_termsim() and upsetplot() by using stable term identifiers internally while keeping display labels readable (2026-06-24, Wed)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)ssplot() (2026-03-02, Mon)dotplot() (2026-02-26, Thu)cnetplot() S3 generic/method consistency warnings (2026-01-14, Wed)treeplot() column selection bug when color variable equals size variable (2026-01-14, Wed)fortify.compareClusterResult() warnings about missing imports and global variables (2026-01-14, Wed)plyr and use dplyr in method-fortify.R (2026-01-14, Wed)treeplot() issue where pairwise_termsim() with method="JC" produced unnamed similarity matrix, causing "undefined column selected" error (2025-01-14)fortify.compareClusterResult() warning "NAs introduced by coercion" when Cluster names are not numeric (2025-01-14)barplot() as fortify() generic in ggplot2 checks for unused arguments in ... (2026-01-14, Wed)categorySize parameter in cnetplot() (2026-01-14, Wed)goplot() as GOSemSim uses cache (2026-01-13, Tue)
gotbl object not found issue (2026-01-13, Tue)geneID, geneInCategory and gseaScores from 'enrichit' (2026-01-12, Mon)update_n() if showCategory is a vector of term names (2026-01-08, Thu)outer() by using Vectorize() (2026-01-08, Thu)cnetplot (2025-11-30, Sun, #338)
emapplot (2025-11-30, Sun)emapplot parameters, 'group', 'group_style' and 'label_group_style' (#339)heatplot() and distinguish tip point size variable for treeplot() through internal parameter size_var (2025-11-23, Sat, #335)ggfun::%<+% (2025-11-18, Tue)ssplot(), treeplot() and get_wordcloud() (2025-11-15, Sat)set_enrichplot_color(transform = 'identity') as default behavior (2025-11-11, Tue)
transform = 'log10' in dotplotset_enrichplot_color(transform = 'identity') in heatplot (2025-11-11, Tue)set_enrichplot_color(transform = 'identity') in cnetplot (2025-11-05, Wed)aes_string/aes_ (2025-10-23, Thu, #332)cnetplot for CompareClusterResult (2025-09-13, Sat, #329)
treeplot with two parameters, leave_fontsize and clade_fontsize (2025-07-12, Sat, #324, #325)
fontsize parameter as it only works for clade_fontsizegseaplot2() (2025-07-12, Sat)
pvalue_table_columnspvalue_table_rownamesgoplot() if ontology is not one of the 'MF', 'CC' or 'BP' (2025-04-28, Mon, clusterProfiler#768)cnetplot() (2025-01-08, Wed, #306)emapplot() (2024-12-12, Thu, #304)ridgeplot() (2024-12-12, Thu, #303)emapplot() now allows passing color to a specific color, e.g., color = "black" (2024-11-29, Fri, #300)emapplot()
ridgeplot() (2024-11-06, Wed, #295)cnetplot() (2024-11-06, Wed)
ggtangle::geom_cnet_label() to label items/genes in independent layer (#194, #266, #267)ridgeplot() when selecting a specific gene set and plotting non-core genes (2024-11-06, Wed, #298)goplot() (2024-10-30, Wed)
emaplot(), goplot(), cnetplot() and ssplot(), all power by 'ggtangle' package (2024-10-24, Thu)ggtangle::cnetplot() (2024-10-24, Thu)drag_network() (2024-10-24, Thu)hplot(): Horizontal plot for GSEA result (2024-08-27, Tue)ridgeplot() (2024-08-19, Mon, clusterProfiler#704)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)ridgeplot(showCategory) : support a vector of Description, not ID(2023-12-1, Fri, #193)ridgeplot() supports passing a vector of selected pathways via the 'showCategory' parameter (2023-11-30, Thu, #193)treeplot() to compatible with the current version of ggtree and ggtreeExtra. (2023-10-28, Sat)set_enrichplot_color(), a helper function to set colors (2023-09-13, Wed)
check_installed() to check package dependency (2023-09-08, Fri, #254)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)cnetplot.compareClusterResult() for only contains one cluster (2023-05-24, Wed, #243)emapplot() for parameter mismatch (2023-02-20, Mon)ridgeplot for error when x@readable == TRUE and length(x@gene2Symbol) = 0 (2022-12-5, Mon)ridgeplot for error when x@readable == TRUE and length(x@gene2Symbol) = 0 (2022-12-5, Mon, #217)cnetplot() for node_label parameter is flipped(2022-12-04, Sun, #216)treeplot() (2022-11-18, Fri)dotplot() and autofacet() for gseaResultList objectemapplot(), centplot() and treeplot() (2022-09-11, Sun)treeplot() (2022-10-1, Sat)treeplot() (2022-10-1, Sat)autofacet to automatically split barplot and dotplot into several facets (2022-09-06, Tue)dotplot method for enrichResultList objecthilight_category, alpha_hilight, alpha_nohilight for cnetplot() and emapplot (2022-09-4, Sun)gsearank() can export result as a table when output = "table" (2022-08-29, Mon, #184)fc_readable() (2022-08-29, Mon, #189)color="NES" to dotplot() for gseaResult object (2022-08-29, Mon, #14)geom_gsea_gene layer (2022-08-25, Thu)geom_gsea_gene layer (2022-08-24, Wed)symbol and pvalue for heatplot.enrichResult() (2022-08-20, Sat)group_category and node_label in ssplot() (2022-07-04, Mon)ssplot() (2022-07-04, Mon)gseaplot() and gseaplot2() return gglist object instead of plotting the figure (2022-05-05, Thu)ridgeplot when x@readable = TRUE (2022-04-30, Sat)treeplot: support passing rel object to offset and offset_tiplab (2022-04-24, Sun)cnetplot.enrichResult to be supported by drag_network(2022-3-6, Sun)drag_network to drag the nodes of networks (2022-2-25, Fri)goplot: goplot.gseaResult need setType slot instead of ontology slot (2022-2-22, Tue)gg object instead of print it in dotplot.compareClusterResult() (2022-01-05, Wed, @altairwei, #160)label_format_tiplab and label_format_cladelab parameters for treeplot(2021-12-24, Fri)gseaplot2(2021-12-4, Sat)utilsep_str_wrap to yulab.utils::str_wrap (2021-10-13, Wed)dotplot, emapplot, cnetplot and treeplot(2021-10-8, Fri)treeplot: add "dotplot" and "heatmap" panels for treeplot(2021-9-15, Wed)dotplot: enable size parameter applicable to other columns of compareClusterResult(2021-9-17, Fri)label_format parameter for heatplot (2021-09-01, Wed)get_ggrepel_segsize function to set segment.size value for ggrepel(2021-08-29, Sun)ep_str_wrap (2021-08-28, Sat)cnetplot now works with a named list (2021-08-23, Mon; clusterProfiler#362)aplot::plot_list instead of cowplot::plot_grid (2021-06-13, Suncolor_category and color_gene parameters for cnetplot(2021-6-11, Fri)showCategory parameter to support character input in dotplot.compareClusterResult(2021-6-10, Thu)ssplot for similarity space plot. (2021-4-22, Thu).emapplot function and replace emapplot_cluster by emapplot(group_category = TRUE)emapplot_cluster.enrichResult when the number of cluster is 2 (2021-2-24, Wed).treeplot: The legend is not the right size (2021-2-6, Sat).dotplot for label_format parameter doesn't work(2021-2-3, Wed).gseaplot2(2021-1-28, Thu)dotplot: replace ggsymbol::geom_symbol with ggstar::geom_star(2021-1-6, Wed)shadowtext for three functions: emapplot, emapplot_cluster and cnetplot. (2021-1-5, Tue)dotplot: supports the use of shapes and line colors to distinguish groups (2021-1-3, Sun)treeplot function (2020-12-29, Tue)get_ww to get_similarity_matrix (2020-12-29, Tue)emapplot related functions to emapplot_utilities.Remapplot and cnetplot when enrichment result is one line (2020-12-26, Sat)pairwise_termsim for the bug of repeated filtering of showCategory(2020-12-23, Wed)showCategory for cnetplot, emapplot, emapplot_cluster when showCategory is a vector of term descriptionsorderBy and decreasing parameters for ridgeplot() (2020-11-19, Thu)
emapplot_cluster() to label cluster in center by default and use ggrepel if setting repel = TRUE (2020-11-08, Mon)
label_format parameter to support formatting label (2020-10-28, Wed)
wordcloud_i (2020-10-15, Thu)pairwise_termsim to calculate similarity of enriched terms (2020-10-09, Fri)
node_label_size parameter to adjust the size of node label in emapplot function (2020-09-18, Fri)emapplot_cluster (2020-09-01, Tue)barplot to remove using coord_flip() (2020-09-10, Thu)cnetplot color scale to tolerate with skewed foldchange (2020-03-13, Fri)
cnetplot for compareClusterResult (compareCluster output) (2019-12-02, Mon)barplot, dotplot and fortify methods of compareClusterResult from clusterProfiler (2019-11-2, Sat)node_label parameter in cnetplot to support selection of subset to be labeled (2019-09-27, Fri)
upsetplot for gseaResult (2019-09-25, Wed)upsetplot based on ggupsetgseadist for plotting logFC distribution of selected gene sets. (2019-06-25, Tue)dotplot supports setting x to other variable, e.g. NES (2019-01-10, Thu)gsearank for plotting ranked list of genes belong to specific gene set
(2018-07-04, Wed)base_size parameter in gseaplot2 (2018-06-21, Thu)pmcplot for plotting pubmed trend (2018-06-14, Thu)ggtable for plotting tablegseaplot2 now accepts a vector of geneSetID (2018-06-13, Wed)emapplot supports showCategory parameter to accept a vector of
Description (2018-05-29, Tue)showCategory parameter for vector of Description in
cnetplot
gseaplot2 that mimic the figure generated by broad institute's GSEA software
(2018-05-28, Mon)cnetplot supports showCategory parameter to accept a vector of
Description
node_label = TRUE parameter in cnetplot (2018-04-08, Sun
)dotplot <2018-03-19, Mon>
dotplotgoplot issue by imporint ggraph <2018-03-12, Mon>
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)upsetplot (2018-01-30, Tue)S4 methods (2018-01-29, Mon)colorEdge parameter in cnetplotggplot2::rel to fix R check (2017-11-28, Tue)heatplot and gseaplot (2017-11-28, Tue)ridgeplot, barplot and dotplot derived from DOSE (2017-11-28, Tue)cnetplot (2017-11-28, Tue)goplot for plotting induced GO DAG (2017-11-27, Mon)emapplot for plotting enrichment map (2017-11-23)