APCluster - An R Package for Affinity Propagation ClusteringIn order to make Affinity Propagation Clustering [Frey & Dueck, 2007] accessible to a wider audience in bioinformatics, we ported the Matlab code published by the authors Frey and Dueck (cf. Affinity Propagation Website) to R.
InstallationThe package is available through CRAN - The Comprehensive R Archive Network (click here to view the archive entry of the package). Therefore, the simplest way to install the package is to enter
install.packages("apcluster")into your R session. If, for what reason ever, you prefer to install the package manually, follow the instructions in the user manual.
The current version of the package is 1.4.3 (released 2016-02-24).
- User Manual: PDF (1.0MB; last updated on 2016-02-24)
- Reference Manual: PDF (254KB; last updated on 2016-02-24; generated automatically from package help pages)
Webinar "Introduction to apcluster"On June 13, 2013, the maintainer of the package, Ulrich Bodenhofer, gave a webinar on the apcluster package. The webinar was hosted by the Orange County R User Group and moderated by its president, Ray DiGiacomo, Jr. The demo uses Version 1.3.2 of the package (released June 11, 2013).
- Complete recording of webinar: YouTube Video (length: 59:17)
- Slides of webinar: PDF (6.6MB)
- R code used in webinar: R code (4KB)
- To load the package, enter "library(apcluster)" in your R session.
- To view the user manual, enter "vignette("apcluster")".
- To do a first example, enter "example(apcluster)".
Citing this packageIf you use this package for research that is published later, you are kindly asked to cite it as follows:
U. Bodenhofer, A. Kothmeier, and S. Hochreiter (2011). APCluster: an R package for affinity propagation clustering. Bioinformatics 27:2463-2464. DOI: 10.1093/bioinformatics/btr406.Moreover, we insist that, any time you use/cite the package, you also cite the original paper in which affinity propagation has been introduced:
B. J. Frey and D. Dueck (2007). Clustering by passing messages between data points. Science, 315:972-976. DOI: 10.1126/science.1136800.
- Version 1.4.3 released 2016-02-24:
- added optional color legend to heatmap plotting; in line with this change, some minor changes to the interface of the heatmap() function
- corresponding updates of help pages and vignette
- Version 1.4.2 released 2015-12-24:
- switched sequence kernel example in vignette from 'kernlab' to 'kebabs' package
- workaround to ensure that all apcluster*() methods are able to process KernelMatrix objects (cf. kebabs package)
- replaced data set ch22Promoters by plain text file (FASTA format) in inst/examples
- bug fix in the heatmap() method
- vignette engine changed from Sweave to knitr
- Version 1.4.1 released 2014-12-09:
- fixes in C++ code of sparse affinity propagation
- Version 1.4.0 released 2014-12-01:
- added apcluster() method for sparse similarity matrices; as a consequence, the package now imports the Matrix package and is now also able to handle non-sparse matrix classes defined by the Matrix package. Moreover, similarity functions supplied to the apcluster() method may now also return any matrix type defined by the Matrix package.
- fix of apcluster() for dense matrices to better support -Inf similarities
- added apclusterK() method for sparse similarity matrices
- preferenceRange() is now an S4 generic; re-implementation in C++ to speed up function; changed handling of -Inf similarities for consistency with sparse version
- added preferenceRange() methods for sparse matrices and dense matrix objects from the Matrix package
- new conversion methods implemented for converting dense similarity matrices to sparse ones and vice versa; consequently, sparseToFull() is marked as deprecated.
- adaptation of heatmap() function for improved handling of -Inf similarities
- adaptations of signatures of '[' and '[[' accessor methods
- renamed help page of methods for computing similarity matrices to 'similarities' in order to avoid confusion with the accessor method similarity()
- corresponding updates of help pages and vignette
- Version 1.3.5 released 2014-06-26:
- memory access fixes in C++ code called from apclusterL()
- minor updates of vignette
- Version 1.3.4 released 2013-06-25:
- added sort() function to rearrange clusters according to sort criterion; note that this is an S3 method (see help page for explanation)
- improvements and bug fixes of apclusterL() method for signature 'matrix,missing'
- performance optimizations of apcluster() and apclusterL()
- plotting of clustering results superimposed in scatter plot matrices now also works for AggExResult objects
- improvements of consistency of error and warning messages
- according adaptations of documentation and vignette
- adapted dependency and linking to Rcpp version 0.11.1 (to avoid issues on Mac OS)
- minor correction of package namespace
- Version 1.3.3 released 2014-02-21:
- adapted dependencies and linking to Rcpp version 0.11.0
- cleared up package dependencies
- Version 1.3.2, released 2013-06-11:
- plotting of clustering results extended to data sets with more than two dimensions (resulting in the clustering result being superimposed in a scatterplot matrix); the variant that plot() can be used to draw a heatmap has been removed. From now on, heatmap() must always be used.
- improved NA handling
- correction of input check in apcluster() and apclusterL() (previously, both functions issued a warning whenever argument p had length > 1)
- corresponding updates and further improvements of help pages and vignette
- Version 1.3.1, released 2013-04-22:
- re-implementation of heatmap() method: dendrograms can now be plotted even for APResult and ExClust objects as well as for cluster hierarchies based on prior clusterings; color bars can now be switched off and colors can be changed by user (by new sideColor argument); dendrograms can be switched on and off (by Rowv and Colv arguments);
- added as.hclust() and as.dendrogram() methods
- added new arguments base, showSamples, and horiz to the plot() method with signature (x="AggExResult", y="missing"); moreover, parameters for changing the appearance of the height axis are now respected as well
- streamlining of methods (redundant definition of inherited methods removed)
- various minor improvements of code and documentation
- Version 1.3.0, released 2013-01-07:
- added Leveraged Affinity Propagation Clustering
- re-implementation of main functions as S4 generic methods in order to facilitate the convenient internal computation of similarity matrices
- for convenience, similarity matrices can be stored as part of clustering results
- heatmap plotting now done by heatmap() which has been defined as S4 generic
- extended interface to functions for computing similarity matrices
- added function corSimMat()
- implementation of length() method for classes APResult, AggExResult, and ExClust
- added accessor function to extract clustering levels from AggExResult objects
- correction of exemplars returned by apcluster() for details=TRUE in slot idxAll of returned APResult object
- when using data stored in a data frame, now categorical columns are explicitly omitted, thereby, avoiding warnings
- plotting of clustering results along with original data (2D only) has been accelerated
- all clustering methods now store their calls into the result objects
- updates and extensions of help pages and vignette
- Version 1.2.1, released 2012-06-12:
- added convenient accessor functions to extracting cluster indices from APResult and ExClust objects
- added a function for coercing an APResult object into an ExClust object
- correction of color bar on the left side of heatmaps (default behavior of RowSideColors parameter changed with R 2.15)
- Version 1.2.0, released 2012-03-26:
- reimplementation of apcluster() in C++ using the Rcpp package which reduces computation times by a factor of 9-10
- obsolete function apclusterLM() removed
- updates of help pages and vignette
- Version 1.1.1, released 2011-09-08:
- updated citation
- minor corrections in help pages and vignette
- Version 1.1.0, released 2011-06-15:
- exemplar-based agglomerative clustering (function aggExCluster()) added
- added various plotting functions, e.g. for dendrograms and heatmaps
- added sequence analysis example to vignette
- extension of vignette according to new functionality
- re-organization of variable names in vignette
- added option 'verbose' to apclusterK()
- numerous minor corrections in help pages and vignette
- Version 1.0.3, released 2011-03-01:
- Makefile in inst/doc eliminated to avoid installation problems
- renamed vignette to "apcluster"
- Version 1.0.2, released 2010-03-19:
- replacement of computation of responsibilities and availabilities in apcluster() by pure matrix operations; traditional implementation according to Frey and Dueck still available as function apclusterLM();
- improved support for named objects
- new function for computing label vectors
- re-organization of package source files and help pages
- Version 1.0.1, released 2010-03-02:
- first public release