add treeplot

Author: huerqiang

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: enrichplot
 Title: Visualization of Functional Enrichment Result
-Version: 1.11.1.993
+Version: 1.11.1.994
 Authors@R: c(
     person(given = "Guangchuang", family = "Yu", email = "[email protected]",   role  = c("aut", "cre"), comment = c(ORCID = "0000-0002-6485-8781")),
     person(given = "Erqiang",     family = "Hu", email = "[email protected]",       role = "ctb"))
@@ -25,7 +25,8 @@ Imports:
     scatterpie,
     shadowtext,
     GOSemSim,
-    magrittr
+    magrittr,
+    ggtree
 Suggests:
     clusterProfiler,
     dplyr,
@@ -43,7 +44,10 @@ Suggests:
     grDevices,
     gridExtra,
     ggnewscale,
-    ggrepel (>= 0.9.0)
+    ggrepel (>= 0.9.0),
+    treeio,
+    scales,
+    tidytree
 VignetteBuilder: knitr
 License: Artistic-2.0
 URL: https://yulab-smu.top/biomedical-knowledge-mining-book/

NAMESPACE

@@ -21,6 +21,7 @@ export(heatplot)
 export(plot_grid)
 export(pmcplot)
 export(ridgeplot)
+export(treeplot)
 export(upsetplot)
 exportMethods(cnetplot)
 exportMethods(dotplot)
@@ -31,6 +32,7 @@ exportMethods(gseaplot)
 exportMethods(heatplot)
 exportMethods(pairwise_termsim)
 exportMethods(ridgeplot)
+exportMethods(treeplot)
 exportMethods(upsetplot)
 import(GOSemSim)
 import(ggraph)
@@ -48,6 +50,7 @@ importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,annotation_custom)
+importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,coord_equal)
 importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,element_blank)
@@ -83,10 +86,12 @@ importFrom(ggplot2,scale_color_discrete)
 importFrom(ggplot2,scale_color_gradient)
 importFrom(ggplot2,scale_color_gradientn)
 importFrom(ggplot2,scale_color_manual)
+importFrom(ggplot2,scale_colour_continuous)
 importFrom(ggplot2,scale_colour_gradient2)
 importFrom(ggplot2,scale_fill_continuous)
 importFrom(ggplot2,scale_fill_discrete)
 importFrom(ggplot2,scale_fill_gradientn)
+importFrom(ggplot2,scale_fill_manual)
 importFrom(ggplot2,scale_size)
 importFrom(ggplot2,scale_size_continuous)
 importFrom(ggplot2,scale_x_continuous)
@@ -109,6 +114,14 @@ importFrom(ggraph,geom_node_label)
 importFrom(ggraph,geom_node_point)
 importFrom(ggraph,geom_node_text)
 importFrom(ggraph,ggraph)
+importFrom(ggtree,`%<+%`)
+importFrom(ggtree,geom_cladelab)
+importFrom(ggtree,geom_inset)
+importFrom(ggtree,geom_tiplab)
+importFrom(ggtree,geom_tippoint)
+importFrom(ggtree,ggtree)
+importFrom(ggtree,groupClade)
+importFrom(ggtree,nodepie)
 importFrom(graphics,barplot)
 importFrom(grid,arrow)
 importFrom(grid,gpar)

NEWS.md

@@ -1,5 +1,6 @@
-# enrichplot 1.11.1.993
+# enrichplot 1.11.1.994
 
++ 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)

R/AllGenerics.R

@@ -267,3 +267,54 @@ setGeneric("ridgeplot",
 ##' @export
 setGeneric("upsetplot", function(x, ...) standardGeneric("upsetplot"))
 
+
+##' Functional grouping tree diagram for enrichment result of 
+##' over-representation test or gene set enrichment analysis.
+##'
+##'
+##' This function visualizes gene sets as a tree.
+##' Gene sets with high similarity tend to cluster together, making it easier
+##' for interpretation.
+##' @title treeplot
+##' @rdname treeplot
+##' @param x enrichment result.
+##' @param showCategory number of enriched terms to display
+##' @param color variable that used to color enriched terms, e.g. pvalue,
+##' p.adjust or qvalue
+##' @param label_format a numeric value sets wrap length, alternatively a
+##' custom function to format axis labels.
+##' @param ... additional parameters
+##' @return ggplot object
+##' @export
+##' @examples
+##' \dontrun{
+##'     library(clusterProfiler)
+##'     library(org.Hs.eg.db)
+##'     library(enrichplot)
+##'     library(GOSemSim)
+##'     library(DOSE)
+##'     data(geneList)
+##'     gene <- names(geneList)[abs(geneList) > 2]
+##'     ego <- enrichGO(gene  = gene,
+##'         universe      = names(geneList),
+##'         OrgDb         = org.Hs.eg.db,
+##'         ont           = "BP",
+##'         pAdjustMethod = "BH",
+##'         pvalueCutoff  = 0.01,
+##'         qvalueCutoff  = 0.05,
+##'         readable      = TRUE)
+##'     d <- godata('org.Hs.eg.db', ont="BP")
+##'     ego2 <- pairwise_termsim(ego, method = "Wang", semData = d)
+##'     treeplot(ego2, showCategory = 30)
+##'     keep <- rownames(ego2@termsim)[c(1:10, 16:20)]
+##'     keep
+##'     treeplot(ego2, showCategory = keep)
+##'     treeplot(ego2, showCategory = 20, 
+##'         group_color = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442"))
+##'    }
+setGeneric("treeplot",
+           function(x, showCategory = 30, color="p.adjust", label_format = 30, ...)
+               standardGeneric("treeplot")
+           )
+           
+