emapplot() (2024-12-12, Thu, #304)ridgeplot() (2024-12-12, Thu, #303)emapplot() now allows passing color to a specific color, e.g., color = "black" (2024-11-29, Fri, #300)emapplot()
ridgeplot() (2024-11-06, Wed, #295)cnetplot() (2024-11-06, Wed)
ggtangle::geom_cnet_label() to label items/genes in independent layer (#194, #266, #267)ridgeplot() when selecting a specific gene set and plotting non-core genes (2024-11-06, Wed, #298)goplot() (2024-10-30, Wed)
emaplot(), goplot(), cnetplot() and ssplot(), all power by 'ggtangle' package (2024-10-24, Thu)ggtangle::cnetplot() (2024-10-24, Thu)drag_network() (2024-10-24, Thu)hplot(): Horizontal plot for GSEA result (2024-08-27, Tue)ridgeplot() (2024-08-19, Mon, clusterProfiler#704)yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)dotplot2 to compare two selected clusters in 'compareClusterResult' object (2024-06-15, Sat)volplot to visualize ORA result using volcano plot (2024-06-13, Thu)ridgeplot(showCategory) : support a vector of Description, not ID(2023-12-1, Fri, #193)ridgeplot() supports passing a vector of selected pathways via the 'showCategory' parameter (2023-11-30, Thu, #193)treeplot() to compatible with the current version of ggtree and ggtreeExtra. (2023-10-28, Sat)set_enrichplot_color(), a helper function to set colors (2023-09-13, Wed)
check_installed() to check package dependency (2023-09-08, Fri, #254)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)cnetplot.compareClusterResult() for only contains one cluster (2023-05-24, Wed, #243)emapplot() for parameter mismatch (2023-02-20, Mon)ridgeplot for error when x@readable == TRUE and length(x@gene2Symbol) = 0 (2022-12-5, Mon)ridgeplot for error when x@readable == TRUE and length(x@gene2Symbol) = 0 (2022-12-5, Mon, #217)cnetplot() for node_label parameter is flipped(2022-12-04, Sun, #216)treeplot() (2022-11-18, Fri)dotplot() and autofacet() for gseaResultList objectemapplot(), centplot() and treeplot() (2022-09-11, Sun)treeplot() (2022-10-1, Sat)treeplot() (2022-10-1, Sat)autofacet to automatically split barplot and dotplot into several facets (2022-09-06, Tue)dotplot method for enrichResultList objecthilight_category, alpha_hilight, alpha_nohilight for cnetplot() and emapplot (2022-09-4, Sun)gsearank() can export result as a table when output = "table" (2022-08-29, Mon, #184)fc_readable() (2022-08-29, Mon, #189)color="NES" to dotplot() for gseaResult object (2022-08-29, Mon, #14)geom_gsea_gene layer (2022-08-25, Thu)geom_gsea_gene layer (2022-08-24, Wed)symbol and pvalue for heatplot.enrichResult() (2022-08-20, Sat)group_category and node_label in ssplot() (2022-07-04, Mon)ssplot() (2022-07-04, Mon)gseaplot() and gseaplot2() return gglist object instead of plotting the figure (2022-05-05, Thu)ridgeplot when x@readable = TRUE (2022-04-30, Sat)treeplot: support passing rel object to offset and offset_tiplab (2022-04-24, Sun)cnetplot.enrichResult to be supported by drag_network(2022-3-6, Sun)drag_network to drag the nodes of networks (2022-2-25, Fri)goplot: goplot.gseaResult need setType slot instead of ontology slot (2022-2-22, Tue)gg object instead of print it in dotplot.compareClusterResult() (2022-01-05, Wed, @altairwei, #160)label_format_tiplab and label_format_cladelab parameters for treeplot(2021-12-24, Fri)gseaplot2(2021-12-4, Sat)utilsep_str_wrap to yulab.utils::str_wrap (2021-10-13, Wed)dotplot, emapplot, cnetplot and treeplot(2021-10-8, Fri)treeplot: add "dotplot" and "heatmap" panels for treeplot(2021-9-15, Wed)dotplot: enable size parameter applicable to other columns of compareClusterResult(2021-9-17, Fri)label_format parameter for heatplot (2021-09-01, Wed)get_ggrepel_segsize function to set segment.size value for ggrepel(2021-08-29, Sun)ep_str_wrap (2021-08-28, Sat)cnetplot now works with a named list (2021-08-23, Mon; clusterProfiler#362)aplot::plot_list instead of cowplot::plot_grid (2021-06-13, Suncolor_category and color_gene parameters for cnetplot(2021-6-11, Fri)showCategory parameter to support character input in dotplot.compareClusterResult(2021-6-10, Thu)ssplot for similarity space plot. (2021-4-22, Thu).emapplot function and replace emapplot_cluster by emapplot(group_category = TRUE)emapplot_cluster.enrichResult when the number of cluster is 2 (2021-2-24, Wed).treeplot: The legend is not the right size (2021-2-6, Sat).dotplot for label_format parameter doesn't work(2021-2-3, Wed).gseaplot2(2021-1-28, Thu)dotplot: replace ggsymbol::geom_symbol with ggstar::geom_star(2021-1-6, Wed)shadowtext for three functions: emapplot, emapplot_cluster and cnetplot. (2021-1-5, Tue)dotplot: supports the use of shapes and line colors to distinguish groups (2021-1-3, Sun)treeplot function (2020-12-29, Tue)get_ww to get_similarity_matrix (2020-12-29, Tue)emapplot related functions to emapplot_utilities.Remapplot and cnetplot when enrichment result is one line (2020-12-26, Sat)pairwise_termsim for the bug of repeated filtering of showCategory(2020-12-23, Wed)showCategory for cnetplot, emapplot, emapplot_cluster when showCategory is a vector of term descriptionsorderBy and decreasing parameters for ridgeplot() (2020-11-19, Thu)
emapplot_cluster() to label cluster in center by default and use ggrepel if setting repel = TRUE (2020-11-08, Mon)
label_format parameter to support formatting label (2020-10-28, Wed)
wordcloud_i (2020-10-15, Thu)pairwise_termsim to calculate similarity of enriched terms (2020-10-09, Fri)
node_label_size parameter to adjust the size of node label in emapplot function (2020-09-18, Fri)emapplot_cluster (2020-09-01, Tue)barplot to remove using coord_flip() (2020-09-10, Thu)cnetplot color scale to tolerate with skewed foldchange (2020-03-13, Fri)
cnetplot for compareClusterResult (compareCluster output) (2019-12-02, Mon)barplot, dotplot and fortify methods of compareClusterResult from clusterProfiler (2019-11-2, Sat)node_label parameter in cnetplot to support selection of subset to be labeled (2019-09-27, Fri)
upsetplot for gseaResult (2019-09-25, Wed)upsetplot based on ggupsetgseadist for plotting logFC distribution of selected gene sets. (2019-06-25, Tue)dotplot supports setting x to other variable, e.g. NES (2019-01-10, Thu)gsearank for plotting ranked list of genes belong to specific gene set
(2018-07-04, Wed)base_size parameter in gseaplot2 (2018-06-21, Thu)pmcplot for plotting pubmed trend (2018-06-14, Thu)ggtable for plotting tablegseaplot2 now accepts a vector of geneSetID (2018-06-13, Wed)emapplot supports showCategory parameter to accept a vector of
Description (2018-05-29, Tue)showCategory parameter for vector of Description in
cnetplot
gseaplot2 that mimic the figure generated by broad institute's GSEA software
(2018-05-28, Mon)cnetplot supports showCategory parameter to accept a vector of
Description
node_label = TRUE parameter in cnetplot (2018-04-08, Sun
)dotplot <2018-03-19, Mon>
dotplotgoplot issue by imporint ggraph <2018-03-12, Mon>
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)upsetplot (2018-01-30, Tue)S4 methods (2018-01-29, Mon)colorEdge parameter in cnetplotggplot2::rel to fix R check (2017-11-28, Tue)heatplot and gseaplot (2017-11-28, Tue)ridgeplot, barplot and dotplot derived from DOSE (2017-11-28, Tue)cnetplot (2017-11-28, Tue)goplot for plotting induced GO DAG (2017-11-27, Mon)emapplot for plotting enrichment map (2017-11-23)