Skip to content

NEWS.md

Latest commit

 

History

History
256 lines (173 loc) · 9.24 KB

NEWS.md

File metadata and controls

256 lines (173 loc) · 9.24 KB

enrichplot 1.17.2

  • autofacet to automatically split barplot and dotplot into several facets (2022-09-06, Tue)
  • dotplot method for enrichResultList object
  • 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
    • YuLab-SMU#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>

    • YuLab-SMU#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)