Changes in version 1.18.1
- fixed issue in treeplot (2022-11-18, Fri, #209)
- enable dotplot() and autofacet() for gseaResultList object(#208)
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)