Package: enrichplot 1.25.0

Guangchuang Yu

enrichplot: Visualization of Functional Enrichment Result

The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualization methods are developed based on 'ggplot2' graphics.

Authors:Guangchuang Yu [aut, cre], Erqiang Hu [ctb], Chun-Hui Gao [ctb]

enrichplot_1.25.0.tar.gz
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enrichplot.pdf |enrichplot.html✨
enrichplot/json (API)
NEWS

# Install 'enrichplot' in R:

install.packages('enrichplot', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/guangchuangyu/enrichplot/issues

On BioConductor:enrichplot-1.25.0(bioc 3.20)enrichplot-1.24.0(bioc 3.19)

bioconductor-package

25 exports 5.17 score 115 dependencies 54 dependents 249 mentions

Last updated 2 months agofrom:e20c821490

Exports:autofacet cnetplot color_palette dotplot drag_network emapplot emapplot_cluster facet_grid geom_gsea_gene ggtable ggtitle goplot gseadist gseaplot gseaplot2 gsearank heatplot pairwise_termsim plot_list pmcplot ridgeplot set_enrichplot_color ssplot treeplot upsetplot

Dependencies:AnnotationDbi ape aplot askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools colorspace cowplot cpp11 crayon curl data.table DBI digest DOSE dplyr fansi farver fastmap fastmatch fgsea formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggtree glue GO.db GOSemSim graphlayouts gridExtra gridGraphics gtable HDO.db httr igraph IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl patchwork pillar pkgconfig plogr plyr png polyclip purrr qvalue R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rlang RSQLite S4Vectors scales scatterpie shadowtext snow stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tidytree treeio tweenr UCSC.utils utf8 vctrs viridis viridisLite withr XVector yulab.utils zlibbioc

Visualization of Functional Enrichment Result

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered fromenrichplot.Rmdusingknitr::rmarkdownon Jun 26 2024.

Last update: 2019-01-10
Started: 2017-11-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
automatically split barplot or dotplot into several facets	autofacet
barplot	barplot.enrichResult
cnetplot	cnetplot cnetplot,compareClusterResult-method cnetplot,enrichResult-method cnetplot,gseaResult-method cnetplot,list-method cnetplot.enrichResult
color_palette	color_palette
dotplot	dotplot dotplot,compareClusterResult,ANY-method dotplot,compareClusterResult-method dotplot,enrichResult-method dotplot,enrichResultList,ANY-method dotplot,enrichResultList-method dotplot,gseaResult-method dotplot,gseaResultList,ANY-method dotplot,gseaResultList-method dotplot.compareClusterResult dotplot.enrichResult
Drag the nodes of a network to update the layout of the network	drag_network
emapplot	emapplot emapplot,compareClusterResult-method emapplot,enrichResult-method emapplot,gseaResult-method emapplot.compareClusterResult emapplot.enrichResult
Functional grouping network diagram for enrichment result of over-representation test or gene set enrichment analysis	emapplot_cluster
fortify	fortify.compareClusterResult fortify.enrichResult
geom_gsea_gene	geom_gsea_gene
ggtable	ggtable
goplot	goplot goplot,enrichResult-method goplot,gseaResult-method goplot.enrichResult
gseadist	gseadist
gseaplot	gseaplot gseaplot,gseaResult-method gseaplot.gseaResult
gseaplot2	gseaplot2
gsearank	gsearank
gsInfo	gsInfo
heatplot	heatplot heatplot,enrichResult-method heatplot,gseaResult-method heatplot.enrichResult
pairwise_termsim	pairwise_termsim pairwise_termsim,compareClusterResult-method pairwise_termsim,enrichResult-method pairwise_termsim,gseaResult-method pairwise_termsim.compareClusterResult pairwise_termsim.enrichResult
plotting-clusterProfile	plotting.clusterProfile
pmcplot	pmcplot
ridgeplot	ridgeplot ridgeplot,gseaResult-method ridgeplot.gseaResult
set_enrichplot_color	set_enrichplot_color
ssplot	ssplot ssplot,compareClusterResult-method ssplot,enrichResult-method ssplot,gseaResult-method ssplot.compareClusterResult ssplot.enrichResult
treeplot	treeplot treeplot,compareClusterResult-method treeplot,enrichResult-method treeplot,gseaResult-method treeplot.compareClusterResult treeplot.enrichResult
upsetplot method	upsetplot upsetplot,enrichResult,ANY-method upsetplot,enrichResult-method upsetplot,gseaResult upsetplot,gseaResult-method