Overview | Adaptive gPCA | Package functionality | Data | Fitting an agpca model | Plotting the output | Interactive choice of $r$ | Correspondence analysis
Package: adaptiveGPCA 0.1.3
adaptiveGPCA: Adaptive Generalized PCA
Implements adaptive gPCA, as described in: Fukuyama, J. (2017) <arxiv:1702.00501>. The package also includes functionality for applying the method to 'phyloseq' objects so that the method can be easily applied to microbiome data and a 'shiny' app for interactive visualization.
Authors:
adaptiveGPCA_0.1.3.tar.gz
adaptiveGPCA_0.1.3.zip(r-4.7-any)adaptiveGPCA_0.1.3.zip(r-4.6-any)adaptiveGPCA_0.1.3.zip(r-4.5-any)
adaptiveGPCA_0.1.3.tgz(r-4.6-any)adaptiveGPCA_0.1.3.tgz(r-4.5-any)
adaptiveGPCA_0.1.3.tar.gz(r-4.7-any)adaptiveGPCA_0.1.3.tar.gz(r-4.6-any)
adaptiveGPCA_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
adaptiveGPCA/json (API)
| # Install 'adaptiveGPCA' in R: |
| install.packages('adaptiveGPCA', repos = c('https://jfukuyama.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jfukuyama/adaptivegpca/issues
Datasets:
- AntibioticPhyloseq - Antibiotic time course experiment.
- AntibioticSmall - A subset of the antibiotic data
Last updated from:a93a3334e3. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 226 | ||
| source / vignettes | OK | 228 | ||
| linux-release | OK | 227 | ||
| macos-release | OK | 266 | ||
| macos-oldrel | OK | 275 | ||
| windows-devel | OK | 174 | ||
| windows-release | OK | 166 | ||
| windows-oldrel | OK | 162 | ||
| wasm-release | OK | 117 |
Exports:adaptivegpcaestimateComponentsgpcagpcaFullFamilyinspectTaxonomyprocessPhyloseqvarianceOnEvecsvisualizeFullFamily
Dependencies:ade4apebase64encBiobaseBiocGenericsbiomformatBiostringsbslibcachemcliclustercodetoolscommonmarkcpp11crayondata.tabledigestfarverfastmapfontawesomeforeachfsgenericsggplot2gluegtablehtmltoolshttpuvigraphIRangesisobanditeratorsjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemulttestnlmeotelpermutephyloseqpixmappkgconfigplyrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangS4VectorsS7sassscalesSeqinfoshinysourcetoolsspstringistringrsurvivalvctrsveganviridisLitewithrxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| adaptiveGPCA: A package for structured dimensionality reduction | adaptiveGPCA-package |
| Adaptive gPCA | adaptivegpca |
| Antibiotic time course experiment. | AntibioticPhyloseq |
| A subset of the antibiotic data | AntibioticSmall |
| Estimate parameters in hierarchical model | estimateComponents |
| gPCA | gpca |
| Make a sequence of ordinations | gpcaFullFamily |
| Shiny gadget for tree/taxonomy inspection | inspectTaxonomy |
| Plot an adaptivegpca object | plot.adaptivegpca |
| Print an adaptivegpca object | print.adaptivegpca |
| Make the input matrices for adaptive gPCA | processPhyloseq |
| Variance along eigenvectors of Q | varianceOnEvecs |
| Shiny gadget for adaptive gPCA | visualizeFullFamily |