NEWS.md

In GuangchuangYu/enrichplot: Visualization of Functional Enrichment Result

enrichplot 1.13.1.992

• 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 1.11.3

• 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)

GuangchuangYu/enrichplot documentation built on Aug. 31, 2021, 7:48 p.m.