NEWS.md

In YuLab-SMU/enrichplot: Visualization of Functional Enrichment Result

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 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)

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)
• 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

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)
• https://github.com/YuLab-SMU/enrichplot/pull/67
• change parameters to be more consistent
• https://github.com/YuLab-SMU/enrichplot/pull/62

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)
• https://github.com/YuLab-SMU/enrichplot/pull/40

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

• 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

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
• https://support.bioconductor.org/p/109438/#109451
• gseaplot2 that mimic the figure generated by broad institute's GSEA software (2018-05-28, Mon)

enrichplot 1.1.1

• cnetplot supports showCategory parameter to accept a vector of Description
• https://github.com/GuangchuangYu/DOSE/issues/20#issuecomment-391802809

enrichplot 1.0.0

• Bioconductor 3.7 release

enrichplot 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

enrichplot 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)

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)

YuLab-SMU/enrichplot documentation built on April 15, 2024, 5:18 p.m.