Introduction | Installation | Getting Started | Adjusting Input Preferences | Exemplar-based Agglomerative Clustering | Leveraged Affinity Propagation | Sparse Affinity Propagation | Processing Biological Sequences | Similarity Matrices | Miscellaneous | Special Notes for Users Upgrading from Previous Versions | How to Cite This Package
Package: apcluster 1.4.14
apcluster: Affinity Propagation Clustering
Implements Affinity Propagation clustering introduced by Frey and Dueck (2007) <doi:10.1126/science.1136800>. The algorithms are largely analogous to the 'Matlab' code published by Frey and Dueck. The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.
Authors:
apcluster_1.4.14.tar.gz
apcluster_1.4.14.zip(r-4.7-x86_64)apcluster_1.4.14.zip(r-4.7-arm64)apcluster_1.4.14.zip(r-4.6-x86_64)apcluster_1.4.14.zip(r-4.6-arm64)apcluster_1.4.14.zip(r-4.5-x86_64)
apcluster_1.4.14.tgz(r-4.6-x86_64)apcluster_1.4.14.tgz(r-4.6-arm64)apcluster_1.4.14.tgz(r-4.5-x86_64)apcluster_1.4.14.tgz(r-4.5-arm64)
apcluster_1.4.14.tar.gz(r-4.7-arm64)apcluster_1.4.14.tar.gz(r-4.7-x86_64)apcluster_1.4.14.tar.gz(r-4.6-arm64)apcluster_1.4.14.tar.gz(r-4.6-x86_64)
apcluster_1.4.14.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
apcluster/json (API)
| # Install 'apcluster' in R: |
| install.packages('apcluster', repos = c('https://ubod.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ubod/apcluster/issues
Last updated from:7c767d7582. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 126 | ||
| linux-devel-x86_64 | OK | 150 | ||
| source / vignettes | OK | 205 | ||
| linux-release-arm64 | OK | 158 | ||
| linux-release-x86_64 | OK | 144 | ||
| macos-release-arm64 | OK | 143 | ||
| macos-release-x86_64 | OK | 256 | ||
| macos-oldrel-arm64 | OK | 125 | ||
| macos-oldrel-x86_64 | OK | 199 | ||
| windows-devel-arm64 | OK | 205 | ||
| windows-devel-x86_64 | OK | 172 | ||
| windows-release-arm64 | OK | 226 | ||
| windows-release-x86_64 | OK | 138 | ||
| windows-oldrel-x86_64 | OK | 138 | ||
| wasm-release | OK | 111 |
Exports:aggExClusterapclusterapclusterDemoapclusterKapclusterLas.dendrogramas.DenseSimilarityMatrixas.hclustas.SparseSimilarityMatrixcorSimMatcutreeexpSimMatheatmaplabelslinKernellinSimMatnegDistMatplotpreferenceRangeshowsimilarity
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| APCluster Package | apcluster-package |
| Exemplar-based Agglomerative Clustering | aggExCluster aggexcluster aggExCluster,character,ANY-method aggExCluster,function,ANY-method aggExCluster,Matrix,ExClust-method aggExCluster,matrix,ExClust-method aggExCluster,Matrix,missing-method aggExCluster,matrix,missing-method aggExCluster,missing,ExClust-method aggExCluster-methods |
| Class "AggExResult" | AggExResult aggexresult AggExResult-class length,AggExResult-method similarity,AggExResult-method [,AggExResult,index,missing,missing-method [[,AggExResult,index,missing-method |
| Affinity Propagation | apcluster apcluster,character,ANY-method apcluster,dgTMatrix,missing-method apcluster,function,ANY-method apcluster,Matrix,missing-method apcluster,matrix,missing-method apcluster,sparseMatrix,missing-method apcluster-methods |
| Affinity Propagation Demo | apclusterDemo |
| Affinity Propagation for Pre-defined Number of Clusters | apclusterK apclusterK,character,ANY-method apclusterK,dgTMatrix,missing-method apclusterK,function,ANY-method apclusterK,Matrix,missing-method apclusterK,matrix,missing-method apclusterK,sparseMatrix,missing-method apclusterK-methods |
| Leveraged Affinity Propagation | apclusterL apclusterL,character,ANY-method apclusterL,function,ANY-method apclusterL,matrix,missing-method apclusterL-methods |
| Class "APResult" | APResult apresult APResult-class length,APResult-method similarity similarity,APResult-method [,APResult,index,missing,missing-method [[,APResult,index,missing-method |
| Coercion of cluster hierarchies | as.dendrogram as.dendrogram,AggExResult-method as.dendrogram,ExClust-method as.hclust as.hclust,AggExResult-method as.hclust,ExClust-method |
| Conversions Between Dense and Sparse Similarity Matrices | as.DenseSimilarityMatrix as.DenseSimilarityMatrix,Matrix-method as.DenseSimilarityMatrix,matrix-method as.DenseSimilarityMatrix,sparseMatrix-method as.DenseSimilarityMatrix-method as.SparseSimilarityMatrix as.SparseSimilarityMatrix,Matrix-method as.SparseSimilarityMatrix,matrix-method as.SparseSimilarityMatrix,sparseMatrix-method as.SparseSimilarityMatrix-methods conversions |
| Cut Out Clustering Level from Cluster Hierarchy | cutree cutree,AggExResult-method cutree,APResult-method cutree-methods |
| Class "ExClust" | ExClust exclust ExClust-class length,ExClust-method similarity,ExClust-method [,ExClust,index,missing,missing-method [[,ExClust,index,missing-method |
| Plot Heatmap | heatmap heatmap,AggExResult,matrix-method heatmap,AggExResult,missing-method heatmap,ExClust,Matrix-method heatmap,ExClust,matrix-method heatmap,ExClust,missing-method heatmap,ExClust,sparseMatrix-method heatmap,matrix,missing-method heatmap,missing,matrix-method heatmap-methods |
| Generate label vector from clustering result | labels labels,APResult-method labels,ExClust-method labels-methods |
| Plot Clustering Results | plot plot,AggExResult,data.frame-method plot,AggExResult,matrix-method plot,AggExResult,missing-method plot,APResult,missing-method plot,ExClust,data.frame-method plot,ExClust,matrix-method plot,ExClust,missing-method plot-methods |
| Determine Meaningful Ranges for Input Preferences | preferenceRange preferenceRange,dgTMatrix-method preferenceRange,Matrix-method preferenceRange,matrix-method preferenceRange,sparseMatrix-method preferenceRange-methods |
| Display Clustering Result Objects | show show,AggExResult-method show,APResult-method show,ExClust-method show-methods |
| Methods for Computing Similarity Matrices | corSimMat expSimMat linKernel linSimMat negDistMat similarities |
| Sort clusters | sort sort,APResult-method sort,ExClust-method sort-methods |