Introduction | Preprocessing | Get pathways | Plot the pathway | Session info
Package: BioCartaImage 1.11.0
Zuguang Gu
BioCartaImage: BioCarta Pathway Images
The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest.
Authors:
BioCartaImage_1.11.0.tar.gz
BioCartaImage_1.11.0.zip(r-4.7)BioCartaImage_1.11.0.zip(r-4.6)BioCartaImage_1.11.0.zip(r-4.5)
BioCartaImage_1.11.0.tgz(r-4.6-any)BioCartaImage_1.11.0.tgz(r-4.5-any)
BioCartaImage_1.11.0.tar.gz(r-4.7-any)BioCartaImage_1.11.0.tar.gz(r-4.6-any)
BioCartaImage_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BioCartaImage/json (API)
| # Install 'BioCartaImage' in R: |
| install.packages('BioCartaImage', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jokergoo/biocartaimage/issues
Datasets:
- BC2ENTREZ - Pre-computed data objects
- BIOCARTA_PATHWAYS - Pre-computed data objects
- PATHWAY2BC - Pre-computed data objects
- PATHWAY2ENTREZ - Pre-computed data objects
- PATHWAY2MSIGDB - Pre-computed data objects
On BioConductor:BioCartaImage-1.11.0(bioc 3.24)BioCartaImage-1.10.0(bioc 3.23)
softwarepathwaysbiocartavisualization
Last updated from:60b13a4d7e. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 177 | ||
| linux-devel-x86_64 | OK | 131 | ||
| source / vignettes | OK | 166 | ||
| linux-release-x86_64 | OK | 137 | ||
| macos-release-arm64 | OK | 129 | ||
| macos-oldrel-arm64 | OK | 109 | ||
| windows-devel | OK | 83 | ||
| windows-release | OK | 76 | ||
| windows-oldrel | OK | 105 | ||
| wasm-release | OK | 111 |
Exports:all_pathwaysBC2ENTREZBIOCARTA_PATHWAYSbiocartaGrobgenes_in_pathwayget_pathwayget_pathway_imagegrid.biocartaimage_dimensionmark_genePATHWAY2BCPATHWAY2ENTREZPATHWAY2MSIGDBpos_by_polygon
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The BioCartaImage package | BioCartaImage-package BioCartaImage |
| All BioCarta pathways | all_pathways |
| Pre-computed data objects | BC2ENTREZ BIOCARTA_PATHWAYS PATHWAY2BC PATHWAY2ENTREZ PATHWAY2MSIGDB |
| Genes in a pathway | genes_in_pathway |
| Get a single pathway | get_pathway |
| Download the pathway image | get_pathway_image image_dimension |
| Draw a BioCarta pathway | biocartaGrob grid.biocarta |
| Internal functions for drawing the pathway grob | grobHeight.biocarta_pathway_grob grobWidth.biocarta_pathway_grob makeContext.biocarta_pathway_grob |
| Mark a gene on the pathway image | mark_gene |
| Position around a polygon | pos_by_polygon |
| Print the biocarta_pathway object | print.biocarta_pathway |
