Changes in version 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) Changes in version 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 Changes in version 1.18.0 - Bioconductor RELEASE_3_16 (2022-11-02, Wed) Changes in version 1.17.4 - rename parameters of emapplot(), centplot() and treeplot() (2022-09-11, Sun) Changes in version 1.17.3 - align the dots in treeplot() (2022-10-1, Sat) - fix a bug in color legend of treeplot() (2022-10-1, Sat) Changes in version 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) Changes in version 1.17.1 - fix a bug in https://github.com/YuLab-SMU/clusterProfiler/issues/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) Changes in version 1.16.0 - Bioconductor 3.15 release Changes in version 1.15.4 - update treeplot: support passing rel object to offset and offset_tiplab (2022-04-24, Sun) Changes in version 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) Changes in version 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) Changes in version 1.15.1 - fixed R check by importing utils Changes in version 1.14.0 - Bioconductor 3.14 release Changes in version 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) Changes in version 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) Changes in version 1.12.0 - Bioconductor 3.13 release Changes in version 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) Changes in version 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 Changes in version 1.11.1 - add orderBy and decreasing parameters for ridgeplot() (2020-11-19, Thu) - https://github.com/YuLab-SMU/enrichplot/pull/84/ - update emapplot_cluster() to label cluster in center by default and use ggrepel if setting repel = TRUE (2020-11-08, Mon) - https://github.com/YuLab-SMU/enrichplot/pull/81 - 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 - https://github.com/YuLab-SMU/enrichplot/pull/73 Changes in version 1.10.0 - Bioconductor 3.12 release (2020-10-28, Wed) Changes in version 1.9.5 - fix wordcloud_i (2020-10-15, Thu) - Remove similarity calculation from emapplot Changes in version 1.9.4 - implement pairwise_termsim to calculate similarity of enriched terms (2020-10-09, Fri) - https://github.com/YuLab-SMU/enrichplot/pull/67 - change parameters to be more consistent - https://github.com/YuLab-SMU/enrichplot/pull/62 Changes in version 1.9.3 - add node_label_size parameter to adjust the size of node label in emapplot function (2020-09-18, Fri) Changes in version 1.9.2 - add function emapplot_cluster (2020-09-01, Tue) Changes in version 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) - https://github.com/YuLab-SMU/enrichplot/pull/40 Changes in version 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) Changes in version 1.6.0 - Bioconductor 3.10 release Changes in version 1.5.2 - update node_label parameter in cnetplot to support selection of subset to be labeled (2019-09-27, Fri) - https://yulab-smu.github.io/clusterProfiler-book/chapter12.html#fig:cnetNodeLabel - upsetplot for gseaResult (2019-09-25, Wed) - reimplement upsetplot based on ggupset Changes in version 1.5.1 - gseadist for plotting logFC distribution of selected gene sets. (2019-06-25, Tue) Changes in version 1.4.0 - Bioconductor 3.9 release Changes in version 1.3.2 - dotplot supports setting x to other variable, e.g. NES (2019-01-10, Thu) - mv vignette to clusterProfiler-book. Changes in version 1.2.0 - Bioconductor 3.8 release Changes in version 1.1.5 - gsearank for plotting ranked list of genes belong to specific gene set (2018-07-04, Wed) Changes in version 1.1.4 - base_size parameter in gseaplot2 (2018-06-21, Thu) Changes in version 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) Changes in version 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 - https://support.bioconductor.org/p/109438/#109451 - gseaplot2 that mimic the figure generated by broad institute's GSEA software (2018-05-28, Mon) Changes in version 1.1.1 - cnetplot supports showCategory parameter to accept a vector of Description - https://github.com/GuangchuangYu/DOSE/issues/20#issuecomment-391802809 Changes in version 1.0.0 - Bioconductor 3.7 release Changes in version 0.99.14 - node_label = TRUE parameter in cnetplot (2018-04-08, Sun ) - drop NA in dotplot <2018-03-19, Mon> - https://twitter.com/S_Canchi/status/974440351162294272 - enable using formula to specify x axis in dotplot Changes in version 0.99.13 - fixed goplot issue by imporint ggraph <2018-03-12, Mon> - https://github.com/GuangchuangYu/enrichplot/issues/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) Changes in version 0.99.9 - defined upsetplot (2018-01-30, Tue) - all visualization methods were defined as S4 methods (2018-01-29, Mon) Changes in version 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)