Affinity Propagation Clustering

Implements Affinity Propagation clustering introduced by Frey and Dueck (2007) . 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.


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.

This is the source code repository. The package can be installed from CRAN. Further information and installation instructions are also available from http://www.bioinf.jku.at/software/apcluster/.

The package is maintained by Ulrich Bodenhofer. The package itself has grown over the years in which multiple students have contributed significant parts: Johannes Palme, Chrats Melkonian, Andreas Kothmeier, and Nikola Kostic

News

Change history of package apcluster:

Version 1.4.7:

  • correction of aggExCluster() C++ code to avoid compilation error on Solaris

Version 1.4.6:

  • aggExCluster() now implemented in C++ instead of R in order to improve speed
  • further correction of conditional loading of package suggested by vignette

Version 1.4.5:

  • loading of suggested Bioconductor packages now performed conditionally to avoid problems when building the package on some platforms that do not have the Bioconductor packages installed

Version 1.4.4:

  • changed dependency to suggested package 'kebabs' to version of at least 1.5.4 for improved interoperability
  • bug fix in as.dendrogram() method with signature 'AggExResult'
  • added discrepancy metric to distance computations and updated src/distanceL.c to new version
  • registered C/C++ subroutines
  • minor change in the vignette template
  • moved NEWS to inst/NEWS
  • added inst/COPYRIGHT

Version 1.4.3:

  • 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:

  • 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.:

  • fixes in C++ code of sparse affinity propagation

Version 1.4.0:

  • 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:

  • memory access fixes in C++ code called from apclusterL()
  • minor updates of vignette

Version 1.3.4:

  • 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:

  • adapted dependencies and linking to Rcpp version 0.11.0
  • cleared up package dependencies

Version 1.3.2:

  • 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:

  • 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:

  • 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:

  • 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:

  • 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:

  • updated citation
  • minor corrections in help pages and vignette

Version 1.1.0:

  • 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:

  • Makefile in inst/doc eliminated to avoid installation problems
  • renamed vignette to "apcluster"

Version 1.0.2:

  • 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:

  • first public release

Reference manual

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install.packages("apcluster")

1.4.7 by Ulrich Bodenhofer, 10 months ago


http://www.bioinf.jku.at/software/apcluster/ https://github.com/UBod/apcluster


Browse source code at https://github.com/cran/apcluster


Authors: Ulrich Bodenhofer , Johannes Palme , Chrats Melkonian , Andreas Kothmeier , Nikola Kostic


Documentation:   PDF Manual  


Task views: Cluster Analysis & Finite Mixture Models


GPL (>= 2) license


Imports Rcpp, methods, Matrix, stats, graphics, grDevices

Suggests Biostrings, kebabs, knitr

Linking to Rcpp


Imported by IPCAPS, NFP, WebGestaltR, diceR, ipft.

Depended on by LPKsample.


See at CRAN