SOM Bound to Realize Euclidean and Relational Outputs

The stochastic (also called on-line) version of the Self-Organising Map (SOM) algorithm is provided. Different versions of the algorithm are implemented, for numeric and relational data and for contingency tables as described, respectively, in Kohonen (2001) , Olteanu & Villa-Vialaneix (2005) and Cottrell et al (2004) . The package also contains many plotting features (to help the user interpret the results) and a graphical user interface based on 'shiny'.


SOMbrero 1.2-3 Fixed bugs: removed unecessary scaling checks for 'relational' in predict

Improvements: used testthat to implement unitary tests remove redundant code in trainSOM fixed seed in unitary tests for reproducibility reasons

Misc: changed message at start (that might be construed as offensive by colorblinds)

SOMbrero 1.2-2 Fixed bugs: fix a bug in plot.somSC for customized colors (reported by Duncan Murdoch) fix a bug in shiny app (downloading CSV files with rownames) fix a bug in 'plot.legend' for SC plot of type 'color'

Improvements: improved rendering of data in shiny app added 'legend' to all SC plots for shiny app added features to display titles (cluster number) in package and shiny app added CSV download for result of the clustering in shiny app

Misc: updated (and improved references) changed maintener's email

SOMbrero 1.2 Fixed bugs: fixed heskes predictions for relation SOM updated scripts for latest igraph version removed predict.somRes for cosine preprocessing (relational)

Code improvements: faster version of dissimilarity SOM as in Mariette et al., 2016

SOMbrero 1.1 Fixed bugs: Changed observation weights in KORRESP: they now correspond to the 2005 KDISJ version and not to the 1993 version Fixed bug when passing proto0 (reported by Renaud Dufour)

Code improvements: changed the function predict.somRes to speed it up

SOMbrero 1.0 (CRAN first release) New features: projectIGraph now handles weighted graphs added a type in plot.somSC that displays a projected graph based on super-graph (see Olteanu & Villa-Vialaneix, Journal de la SFdS, 2015)

Fixed bugs: Fixed a bug related to proto0 when type was not set in trainSOM Fixed a bug in summary.somSC when the number of clusters is not chosen yet Removed parameter 'view' that was not used in internal function 'plotAdd'

Misc: Changed default neighbourhood to Gaussian. The default parameters for this neighbourhood are those already implemented in the R package 'yasomi' Changed the internal function projGraph to handle projection for the SOM grid and for the super-clustering in a single function Added the neighborhood type of the SOM in method print for the class somRes

SOMbrero 0.5 New features: Added an option for affectation type ("standard"/hard or "heskes"/soft affectation) Updated shiny interface accordingly

Fixed bugs: Fixed a bug related to dist.type in selectNei. This bug did not affect the learning in previous versions but could provide false values for protoDist after the training.

SOMbrero 0.4-2 New features: Added PCA initialization Added Gaussian neighborhood (default parameters are still tentative) Added cosinus normalization for dissimilarity Added ANOVA like analyses for relational SOM interpretation Included a function to project an 'igraph' object on the grid

Fixed bugs: Fixed a bug in the computation of projected graph. Only edges with non zero counts for the number of links are now listed in the edge list.

Misc: Added tests: to check the equivalence between automatic and manual scaling and the equivalence between predicted clustering and the output of predict Updated vignettes

SOMbrero 0.4-1 New features: Added a parameter that tunes the gradient descent step Added a web user interface, implemented with shiny Added the topographic error to somRes.summary Improved the summary of somSC (table of neuron numbers and superclass numbers)

Code improvements: Changed default value of init.proto to "obs" for "relational" algorithm

Fixed bugs: Changed scree plot title and ylabel to "proportion of unexplained variables"

Misc: Added test: equivalence of numeric SOM and relational SOM on squared euclidian distance

SOMbrero 0.4 New features: Implementation of the "dissimilarity" algorithm to handle dissimilarity data Plots, quality functions and super-clustering have been updated to handle this case

Code improvements: New way to handle distance calculations New way to handle the 'korresp' preprocessing (full matrix is now included) Slightly changed default values for Letremy's radius and neighborhood: they are now exactly the same than in the original programs

Fixed bugs: Fixed bug with default options in korresp case Fixed bug with affectation step in korresp case Fixed bug for what="add" and type="graph" (node sizes were wrong)

Misc: Added markdown vignettes: one general and one for each case; hence, the package now depends on R version 3.0 or higher Added citation file Added demos Removed unecessary tests and examples

SOMbrero 0.3 New features: Implementation of the "korresp" algorithm to handle contingency table Plots, quality functions and super-clustering have been updated to handle this case

Fixed bugs: Bug fixed in the dendrogram of super-clustering (percentage of explained variance was incorrectly displayed) Bug fixed in smooth.dist and umatrix (distances were reversed)

SOMbrero 0.2-2 New options: The argument 'the.titles' has been introduced in plot.somRes

New features: Implementation of a quality function for somRes object Implementation of a super-clustering for the resulting prototypes Implementation of a plot method for the results of the super-clustering

SOMbrero 0.2 Name changes : The argument 'scale' of 'somRes' object is now called 'scaling' (conflict with a R base function)

Argument changes : The argument 'dist.type' has been transfered from 'somRes' to 'myGrid' objects.

New options: Distance type on the grid : maximum, euclidean, manhattan, canberra, binary or minkowski New plots: Observations : color, lines, barplot, radar, boxplot and names Prototypes : lines, barplot, radar, 3d, poly.dist, umatrix and smooth.disy Additional variable : pie, color, lines, barplot, radar, boxplot, words, names and graph

SOMbrero 0.1 The initial version of onlineSOM package considers only numerical data.

Available parameters of the SOM algorithm: Grid : square topology SOM type : numeric SOM mode : online Radius type : letremy Prototypes initialization : random or obs Scale : unitvar, center or none

Available plots: Observations : hitmap Prototypes : color Energy

Reference manual

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1.2-3 by Nathalie Villa-Vialaneix, a year ago

Report a bug at

Browse source code at

Authors: Nathalie Villa-Vialaneix [aut, cre] , Jerome Mariette [aut] , Madalina Olteanu [aut] , Fabrice Rossi [aut] , Laura Bendhaiba [ctb] , Julien Boelaert [ctb]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports wordcloud, scatterplot3d, RColorBrewer, shiny, grDevices, graphics, stats

Depends on igraph

Suggests testthat, rmarkdown, knitr

Imported by GenomicMating.

See at CRAN