Introduction | Pathway | Plot the pathway using ggraph | Converting identifiers | Highlighting set of nodes and edges | Overlaying raw KEGG image | Module and Network | Parsing module | Visualizing module | Use with the other omics packages | Wrapper function ggkegg
Package: ggkegg 1.11.0
Noriaki Sato
ggkegg: Analyzing and visualizing KEGG information using the grammar of graphics
This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.
Authors:
ggkegg_1.11.0.tar.gz
ggkegg_1.11.0.zip(r-4.7)ggkegg_1.11.0.zip(r-4.6)ggkegg_1.11.0.zip(r-4.5)
ggkegg_1.11.0.tgz(r-4.6-any)ggkegg_1.11.0.tgz(r-4.5-any)
ggkegg_1.11.0.tar.gz(r-4.7-any)ggkegg_1.11.0.tar.gz(r-4.6-any)
ggkegg_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggkegg/json (API)
| # Install 'ggkegg' in R: |
| install.packages('ggkegg', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/noriakis/ggkegg/issues
On BioConductor:ggkegg-1.11.0(bioc 3.24)ggkegg-1.10.0(bioc 3.23)
pathwaysdataimportkeggggplot2ggraphpathwaytidygraphvisualization
Last updated from:b197ce98c3. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 195 | ||
| linux-devel-x86_64 | NOTE | 321 | ||
| source / vignettes | OK | 264 | ||
| linux-release-x86_64 | NOTE | 345 | ||
| macos-release-arm64 | NOTE | 159 | ||
| macos-oldrel-arm64 | NOTE | 155 | ||
| windows-devel | NOTE | 193 | ||
| windows-release | NOTE | 194 | ||
| windows-oldrel | NOTE | 226 | ||
| wasm-release | OK | 169 |
Exports:add_readable_edge_labeladd_titleappend_cpappend_label_positionassign_deseq2carrowcombine_with_bnlearnconvert_idcreate_test_modulecreate_test_networkcreate_test_pathwayedge_matrixedge_numericedge_numeric_sumgeom_kegggeom_node_rectgeom_node_rect_kegggeom_node_rect_multigeom_node_shadowtextget_module_attributeget_network_attributeggkeggggkeggsaveggplot_add.add_readable_edge_labelggplot_add.geom_keggggplot_add.geom_node_rect_keggggplot_add.geom_node_rect_multiggplot_add.overlay_raw_maphighlight_entitieshighlight_modulehighlight_set_edgeshighlight_set_nodesmodulemodule_abundancemodule_completenessmodule_textmulti_pathway_nativenetworknetwork_graphnode_matrixnode_numericobtain_sequential_module_definitionoutput_overlay_imageoverlay_raw_mappathwaypathway_abundancepathway_infoplot_kegg_networkplot_module_blocksplot_module_textprocess_lineprocess_reactionrawMaprawValuereturn_line_compoundsstamp
Dependencies:askpassbase64encBiocFileCachebitbit64blobbslibcachemclicpp11curldata.tableDBIdbplyrdigestdplyrevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggforceggiraphggplot2ggraphggrepelgluegraphlayoutsgridExtragtablehighrhtmltoolshtmlwidgetshttr2igraphisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagickmagrittrMASSMatrixmemoisemimeopensslpatchworkpillarpkgconfigpolyclippurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownRSQLiteS7sassscalesshadowtextstringistringrsyssystemfontstibbletidygraphtidyrtidyselecttinytextweenrutf8vctrsviridisviridisLitewithrxfunXMLyaml
