Package: enrichplot 1.33.0
Guangchuang Yu
enrichplot: Visualization of Functional Enrichment Result
The 'enrichplot' package provides visualization methods for interpreting functional enrichment results from ORA or GSEA analyses. It is designed to work with the 'clusterProfiler' ecosystem and builds on 'ggplot2' for flexible and extensible graphics.
Authors:
enrichplot_1.33.0.tar.gz
enrichplot_1.33.0.zip(r-4.7)enrichplot_1.33.0.zip(r-4.6)enrichplot_1.33.0.zip(r-4.5)
enrichplot_1.33.0.tgz(r-4.6-any)enrichplot_1.33.0.tgz(r-4.5-any)
enrichplot_1.33.0.tar.gz(r-4.7-any)enrichplot_1.33.0.tar.gz(r-4.6-any)
enrichplot_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-1.33.0(bioc 3.24)enrichplot-1.32.0(bioc 3.23)
annotationgenesetenrichmentgokeggpathwayssoftwarevisualizationenrichment-analysispathway-analysisquarto
Last updated from:8adce9ad89. Checks:8 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 247 | ||
| linux-devel-x86_64 | ERROR | 432 | ||
| source / vignettes | OK | 242 | ||
| linux-release-x86_64 | ERROR | 324 | ||
| macos-release-arm64 | ERROR | 227 | ||
| macos-oldrel-arm64 | ERROR | 168 | ||
| windows-devel | ERROR | 231 | ||
| windows-release | ERROR | 223 | ||
| windows-oldrel | ERROR | 201 | ||
| wasm-release | OK | 187 |
Exports:autofacetcnetplotcolor_palettedotplotdotplot2emapplotfacet_gridgeneIDgeneInCategorygeom_cnet_labelgeom_gsea_geneget_enrichplot_colorggtableggtitlegoplotgseadistgseaplotgseaplot2gsearankgseaScoresheatplothplotmanhattanplotpairwise_termsimplot_listpmcplotridgeplotset_enrichplot_colorssplottheme_dosetreeplotupsetplotvolplot
Dependencies:AnnotationDbiapeaplotaskpassbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemcliclustercpp11crayoncurlDBIdigestDOSEdplyrenrichitevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgridGraphicsgtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemimenlmeopensslpatchworkpillarpkgconfigplyrpngpolyclippurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownRSQLiteS4VectorsS7sassscalesscatterpieSeqinfostringistringrsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextreeiotweenrutf8vctrsviridisLitewithrxfunXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert compareClusterResult to data frame | as.data.frame.compareClusterResult |
| Plotting utility functions for enrichplot package | autofacet |
| barplot | barplot.enrichResult |
| Category-Gene-Network Plot | cnetplot.compareClusterResult cnetplot.enrichResult cnetplot.gseaResult |
| Create color palette for continuous data | 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 |
| dotplot2 | dotplot2 |
| emapplot | emapplot emapplot,compareClusterResult-method emapplot,enrichResult-method emapplot,gseaResult-method emapplot_internal |
| Predefined color palettes | enrichplot_point_shape |
| fortify | fortify.compareClusterResult fortify.enrichResult |
| geom_gsea_gene | geom_gsea_gene |
| Color utility functions for enrichplot package | get_enrichplot_color |
| ggtable | ggtable |
| goplot | goplot goplot,enrichResult-method goplot,gseaResult-method |
| 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 |
| hplot | hplot |
| manhattanplot | manhattanplot manhattanplot,compareClusterResult,ANY-method manhattanplot,compareClusterResult-method manhattanplot,enrichResult-method manhattanplot,enrichResultList,ANY-method manhattanplot,enrichResultList-method manhattanplot,gseaResult-method manhattanplot,gseaResultList,ANY-method manhattanplot,gseaResultList-method manhattanplot,list,ANY-method manhattanplot,list-method |
| pairwise_termsim | pairwise_termsim pairwise_termsim,compareClusterResult-method pairwise_termsim,enrichResult-method pairwise_termsim,gseaResult-method pairwise_termsim.compareClusterResult pairwise_termsim.enrichResult |
| Internal plot function for plotting compareClusterResult | plotting.clusterProfile |
| pmcplot | pmcplot |
| ridgeplot | ridgeplot ridgeplot,gseaResult-method ridgeplot.gseaResult |
| Helper function to set color scale for enrichplot | 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_internal |
| upsetplot method | upsetplot upsetplot,enrichResult,ANY-method upsetplot,enrichResult-method upsetplot,gseaResult upsetplot,gseaResult-method |
| volplot | volplot volplot,enrichResult-method volplot.enrichResult |
