\documentclass[article]{bioinf}

\usepackage{amsmath,amssymb}
\usepackage{hyperref}

\hypersetup{colorlinks=false,
   pdfborder=0 0 0,
   pdftitle={APCluster - An R Package for Affinity Propagation Clustering},
   pdfauthor={Ulrich Bodenhofer}}

\title{{\Huge APCluster}\\[5mm]
  An R Package for Affinity Propagation Clustering}
\author{Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, and Andreas Kothmeier}
\affiliation{Institute of Bioinformatics, Johannes Kepler University
Linz\\Altenberger Str. 69, 4040 Linz, Austria\\
\email{apcluster@bioinf.jku.at}}

\newcommand{\APCluster}{\texttt{apcluster}}
\newcommand{\KeBABS}{\texttt{kebabs}}
\newcommand{\R}{R}
\newcommand{\Real}{\mathbb{R}}

\renewcommand{\vec}[1]{\mathbf{#1}}

%\VignetteIndexEntry{An R Package for Affinity Propagation Clustering}
%\VignetteDepends{methods, stats, graphics, utils}
%\VignetteEngine{knitr::knitr}

\begin{document}
<<Init,echo=FALSE,message=FALSE,results='hide'>>=
options(width=72)
knitr::opts_knit$set(width=72)
set.seed(0)
suggestedPackages <- c("Biostrings", "kebabs")
if (all(sapply(suggestedPackages, requireNamespace, quietly=TRUE))) {
    library(kebabs, quietly=TRUE)
} else {
    knitr::opts_chunk$set(eval=FALSE)
}
library(apcluster, quietly=TRUE)
apclusterVersion <- packageDescription("apcluster")$Version
apclusterDateRaw <- packageDescription("apcluster")$Date
apclusterDateYear <- as.numeric(substr(apclusterDateRaw, 1, 4))
apclusterDateMonth <- as.numeric(substr(apclusterDateRaw, 6, 7))
apclusterDateDay <- as.numeric(substr(apclusterDateRaw, 9, 10))
apclusterDate <- paste(month.name[apclusterDateMonth], " ",
                     apclusterDateDay, ", ",
                     apclusterDateYear, sep="")
@
\newcommand{\APClusterVer}{\Sexpr{apclusterVersion}}
\newcommand{\APClusterDate}{\Sexpr{apclusterDate}}
\manualtitlepage[Version \APClusterVer, \APClusterDate]

\section*{Scope and Purpose of this Document}

This document is a user manual for the \R\ package \APCluster\
\cite{BodenhoferKothmeierHochreiter11}.
It is only meant as a gentle introduction into how to use the basic
functions implemented in this package. Not all features of the \R\
package are described in full detail. Such details can be obtained
from the documentation enclosed in the  \R\ package. Further note
the following: (1) this is neither an introduction to affinity propagation
nor to clustering in general; (2) this is not an introduction to \R.
If you lack the background for understanding this manual, you first
have to read introductory literature on these subjects.

\newpage

\vspace{1cm}

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\tableofcontents
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\newcommand{\notebox}[1]{%
\begin{center}
\fbox{\begin{minipage}{\Nboxwidth}
\noindent{\sffamily\bfseries Note:} #1
\end{minipage}}
\end{center}}

\section{Introduction}

Affinity propagation (AP) is a relatively new clustering algorithm
that has been introduced by Brendan J.\ Frey and Delbert Dueck
\cite{FreyDueck07}.\footnotemark[1]\footnotetext[1]{%
\url{http://www.psi.toronto.edu/affinitypropagation/}}\stepcounter{footnote}
The authors themselves describe affinity propagation as
follows:\footnote{quoted from
\url{http://www.psi.toronto.edu/affinitypropagation/faq.html\#def}}

\begin{quote}
``{\em An algorithm that identifies
exemplars among data points and forms clusters of data points
around these exemplars. It operates by simultaneously
considering all data point as potential exemplars and
exchanging messages between data points until a good set of
exemplars and clusters emerges.}''
\end{quote}

AP has been applied in various fields recently, among which bioinformatics
is becoming increasingly important. Frey and Dueck have made their algorithm
available as Matlab code.\footnotemark[1] Matlab,
however, is relatively uncommon in bioinformatics. Instead, the statistical
computing platform \R\ has become a widely accepted standard in this field.
In order to leverage affinity propagation for bioinformatics applications,
we have implemented affinity propagation as an \R\ package.
Note, however, that the given package is in no way restricted
to bioinformatics applications. It is as generally applicable as Frey's and
Dueck's original Matlab code.\footnotemark[1]

Starting with Version 1.1.0, the \APCluster\ package also features
{\em exemplar-based agglomerative clustering} which can be used as a clustering
method on its own or for creating a hierarchy of clusters that have been
computed previously by affinity propagation.
{\em Leveraged Affinity Propagation}, a variant of AP especially geared to
applications involving large data sets, has first been included in Version
1.3.0.

\section{Installation}

\subsection{Installation via CRAN}

The \R\ package \APCluster\ (current version: \APClusterVer) is
part of the {\em Comprehensive R Archive Network (CRAN)}%
\footnote{\url{http://cran.r-project.org/}}. The simplest way to install the
package, therefore, is to enter the following command into your \R\ session:
<<InstallAPCluster,eval=FALSE>>=
install.packages("apcluster")
@
If you use R on Windows or Mac OS, you can also conveniently use the package
installation menu of your R GUI.

\subsection{Manual installation from source}

Under special circumstances, e.g. if you want to compile
the C++ code included in the package with some custom options,
you may prefer to install the package manually from source.
To this end, open the package's page at CRAN%
\footnote{\url{http://cran.r-project.org/web/packages/apcluster/index.html}} and
then proceed as follows:
\begin{enumerate}
\item Download \texttt{apcluster\_\APClusterVer.tar.gz}
and save it to your harddisk.
\item Open a shell/terminal/command prompt window and change to the directory where you put
  {\ttfamily apcluster\_\APClusterVer.tar.gz}. Enter
\begin{quote}
\ttfamily R CMD INSTALL apcluster\_\APClusterVer.tar.gz
\end{quote}
to install the package.
\end{enumerate}
Note that this might require additional software on some platforms. Windows requires
Rtools\footnote{\url{http://cran.r-project.org/bin/windows/Rtools/}} to be installed and
to be available in the default search path (environment variable \verb+PATH+).
Mac OS X requires Xcode developer tools%
\footnote{\url{https://developer.apple.com/technologies/tools/}} (make sure that
you have the command line tools installed with Xcode).

\subsection{Compatibility issues}

All versions downloadable from CRAN have been built using the latest version, \R\
\Sexpr{R.version$major}.\Sexpr{R.version$minor}.
However, the package should work without severe problems on \R\ versions $\geq$3.0.0.

\section{Getting Started}

To load the package, enter the following in your \R\ session:
<<LoadAPCluster,eval=FALSE>>=
library(apcluster)
@
If this command terminates without any error
message or warning, you can be sure that the package has
been installed successfully. If so, the package is ready
for use now and you can start clustering your data with affinity propagation.

The package includes both a user manual (this document) and a reference manual
(help pages for each function). To view the user manual, enter
<<OpenVignette,eval=FALSE>>=
vignette("apcluster")
@
Help pages can be viewed using the \verb+help+ command. It is recommended to
start with
<<ShowHelp,eval=FALSE>>=
help(apcluster)
@

Affinity propagation does not require the data samples to be of any
specific kind or structure. AP only requires a {\em similarity matrix}, i.e.,
given $l$ data samples, this is an $l\times l$ real-valued matrix $\mathbf{S}$,
in which an entry $S_{ij}$ corresponds to a value measuring how similar
sample $i$ is to sample $j$. AP does not require these values to be in a
specific range. Values can be positive or negative. AP does not
even require the similarity matrix to be symmetric (although, in most
applications, it will be symmetric anyway). A value of $-\infty$ is interpreted
as ``absolute dissimilarity''. The higher a value, the more similar two samples
are considered.

To get a first impression, let us create a random data set in
$\Real^2$ as the union of two ``Gaussian clouds'':
\begin{center}
<<CreateDataSet1,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
cl1 <- cbind(rnorm(30, 0.3, 0.05), rnorm(30, 0.7, 0.04))
cl2 <- cbind(rnorm(30, 0.7, 0.04), rnorm(30, 0.4, .05))
x1 <- rbind(cl1, cl2)
plot(x1, xlab="", ylab="", pch=19, cex=0.8)
@
\end{center}
The package \APCluster\ offers several different ways for clustering data.
The simplest way is the following:
<<APClusterDataSet1>>=
apres1a <- apcluster(negDistMat(r=2), x1)
@
In this example, the function \verb+apcluster()+ first computes a similarity
matrix for the input data \verb+x1+ using the {\em similarity function}
passed as first argument. The choice \verb+negDistMat(r=2)+ is the standard
similarity measure used in the papers of Frey and Dueck ---
negative squared distances.

Alternatively, one can compute the similarity matrix beforehand and call
\verb+apcluster()+ for the similarity matrix (for a more detailed description
of the differences, see \ref{ssec:memeff}):
<<APClusterDataSet1b>>=
s1 <- negDistMat(x1, r=2)
apres1b <- apcluster(s1)
@

The function \verb+apcluster()+ creates an object belonging to the S4
class \verb+APResult+ which is defined by the present package. To get
detailed information on which data are stored in such objects, enter
<<ShowHelpAPResult,eval=FALSE>>=
help(APResult)
@
The simplest thing we can do is to enter the name of the
object (which implicitly calls \verb+show()+) to get a summary of the
clustering result:
<<ShowResultAPClusterDataSet1>>=
apres1a
@
The \APCluster\ package allows for plotting the
original data set along with a clustering result:
\begin{center}
<<PlotResultAPClusterDataSet1,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
plot(apres1a, x1)
@
\end{center}
In this plot, each color corresponds to one cluster. The exemplar of each
cluster is marked by a box and all cluster members are connected to their
exemplars with lines.

A heatmap is plotted with \verb+heatmap()+:
\begin{center}
<<HeatmapResultAPClusterDataSet1,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(apres1a)
@
\end{center}
In the heatmap, the samples are grouped according to clusters. The above
heatmap confirms again that there are two main clusters in the data.
A heatmap can be plotted for the object \verb+apres1a+ because
\verb+apcluster()+, if called for data and a similarity function, by default
includes the similarity matrix in the output object (unless it was called
with the switch \verb+includeSim=FALSE+). If the similarity matrix is not
included (which is the default if \verb+apcluster()+ has been called on a
similarity matrix directly), \verb+heatmap()+ must be called with the
similarity matrix as second argument:
\begin{center}
<<HeatmapResultAPClusterDataSet1b,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(apres1b, s1)
@
\end{center}

Suppose we want to have better insight into what the algorithm did in each
iteration. For this purpose, we can supply the option \verb+details=TRUE+
to \verb+apcluster()+:
<<APClusterDataSet1Details>>=
apres1c <- apcluster(s1, details=TRUE)
@
This option tells the algorithm to keep a detailed log about its progress.
For example, this allows for plotting the three performance measures that AP
uses internally for each iteration:
\begin{center}
<<PlotAPClusterDataSet1Details,fig.width=6,fig.height=4,out.width='0.5\\textwidth'>>=
plot(apres1c)
@
\end{center}
These performance measures are:
\begin{enumerate}
\item Sum of exemplar preferences
\item Sum of similarities of exemplars to their cluster members
\item Net fitness: sum of the two former
\end{enumerate}
For details, the user is referred to the original affinity propagation
paper \cite{FreyDueck07} and the supplementary material published on the
affinity propagation Web page.\footnotemark[1] We see
from the above plot that the algorithm has not made any change for the last 100
(of \Sexpr{apres1b@it}!) iterations. AP, through its parameter
\verb+convits+, allows to
control for how long AP waits for a change until it terminates (the default is
\verb+convits=100+). If the user has the feeling that AP will probably
converge quicker on his/her data set, a lower value can be used:
<<APClusterDataSet1convits15>>=
apres1c <- apcluster(s1, convits=15, details=TRUE)
apres1c
@

\section{Adjusting Input Preferences}\label{sec:ipref}

Apart from the similarity matrix itself, the most important input parameter of
AP is the so-called {\em input preference} which can be interpreted as the
tendency of a data sample to become an exemplar (see \cite{FreyDueck07} and
supplementary material on the AP homepage\footnotemark[1] for a more detailed
explanation). This input preference can either be chosen individually for
each data sample or it can be a single value shared among all data samples.
Input preferences largely determine the number of clusters,
in other words, how fine- or coarse-grained the clustering result will be.

The input preferences one can specify for AP are roughly in the same range
as the similarity values, but they do not have a straightforward interpretation.
Frey and Dueck have introduced the following rule of thumb: ``{\it The shared
value could be the median of the input similarities (resulting in a moderate
number of clusters) or their minimum (resulting in a small number of
clusters).}'' \cite{FreyDueck07}

Our AP implementation uses the median rule by default if the user does not
supply a custom value for the input preferences. In order to provide the user
with a knob that is --- at least to some extent --- interpretable, the function
\verb+apcluster()+ provides an argument \verb+q+ that allows to set the input
preference to a certain quantile of the input similarities: resulting in the
median for \verb+q=0.5+ and in the minimum for \verb+q=0+. As an example, let
us add two more ``clouds'' to the data set from above:
\begin{center}
<<CreateDataSet2,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
cl3 <- cbind(rnorm(20, 0.50, 0.03), rnorm(20, 0.72, 0.03))
cl4 <- cbind(rnorm(25, 0.50, 0.03), rnorm(25, 0.42, 0.04))
x2 <- rbind(x1, cl3, cl4)
plot(x2, xlab="", ylab="", pch=19, cex=0.8)
@
\end{center}
For the default setting, we obtain the following result:
\begin{center}
<<APClusterDataSet2,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
apres2a <- apcluster(negDistMat(r=2), x2)
plot(apres2a, x2)
@
\end{center}
For the minimum of input similarities, we obtain the following result:
\begin{center}
<<APClusterDataSet2q0,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
apres2b <- apcluster(negDistMat(r=2), x2, q=0)
plot(apres2b, x2)
@
\end{center}
So we see that AP is quite robust against a reduction of input preferences
in this example which may be caused by the clear separation of the four
clusters. If we increase input preferences, however, we can force AP to
split the four clusters into smaller sub-clusters:
\begin{center}
<<PlotAPClusterDataSet2q08,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
apres2c <- apcluster(negDistMat(r=2), x2, q=0.8)
plot(apres2c, x2)
@
\end{center}

Note that the input preference used by AP can be recovered from the output
object (no matter which method to adjust input preferences has been used).
On the one hand, the value is printed if the object is displayed
(by \verb+show+ or by entering the output object's name). On the other hand,
the value can be accessed directly via the slot \verb+p+:
<<APClusterDataSet2q08showp>>=
apres2c@p
@

As noted above already, we can produce a heatmap by calling \verb+heatmap()+
for an \verb+APResult+ object:
\begin{center}
<<HeatmapResultAPClusterDataSet2q08,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(apres2c)
@
\end{center}
The order in which the clusters are arranged in the heatmap is determined
by means of joining the cluster agglomeratively (see Section \ref{sec:agglo}
below). Although the affinity propagation result contains
\Sexpr{length(apres2c@exemplars)} clusters, the heatmap indicates that
there are actually four clusters which can be seen as very brightly
colored squares along the diagonal. We also see that there seem to be
two pairs of adjacent clusters, which can be seen from the fact
that there are two relatively light-colored blocks along the diagonal
encompassing two of the four clusters in each case. If we look back at
how the data have been created (see also plots above), this is exactly
what is to be expected.

The above example with \verb+q=0+ demonstrates that setting
input preferences to the minimum of input similarities does not necessarily
result in a very small number of clusters (like one or two). This is due to the
fact that input preferences need not necessarily be exactly in the range of the
similarities. To determine a meaningful range, an auxiliary function is
available which, in line with Frey's and Dueck's Matlab code,\footnotemark[1]
allows to compute
a minimum value (for which one or at most two clusters would be obtained)
and a maximum value (for which as many clusters as data samples would be
obtained):
<<PreferenceRangeDataSet2>>=
preferenceRange(apres2b@sim)
@
The function returns a two-element vector with the minimum value as first and
the maximum value as second entry. The computations are done approximately
by default. If one is interested in exact bounds, supply \verb+exact=TRUE+
(resulting in longer computation times).

Many clustering algorithms need to know a pre-defined number of clusters. This
is often a major nuisance, since the exact number of clusters is hard to know
for non-trivial (in particular, high-dimensional) data sets. AP avoids this
problem. If, however, one still wants to require a fixed number of clusters,
this has to be accomplished by a search algorithm that adjusts input preferences
in order to produce the desired number of clusters in the end. For convenience,
this search algorithm is available as a function \verb+apclusterK()+
(analogous to Frey's and Dueck's Matlab implementation\footnotemark[1]).
We can use this function to
force AP to produce only two clusters (merging the two pairs of adjacent
clouds into one cluster each). Analogously to \verb+apcluster()+,
\verb+apclusterK()+ supports two variants --- it can either be called
for a similarity measure and data or on a similarity matrix directly.
\begin{center}
<<APClusterKDataSet2,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
apres2d <- apclusterK(negDistMat(r=2), x2, K=2, verbose=TRUE)
plot(apres2d, x2)
@
\end{center}

Now let us quickly consider a simple data set with more than two features. The
notorious example is Fisher's iris data set:
<<IrisData1>>=
data(iris)
apIris1 <- apcluster(negDistMat(r=2), iris)
apIris1
@
AP has identified \Sexpr{length(apIris1)} clusters. Since Version 1.3.2, the
package also allows for superimposing clustering results in scatter plot matrices:
\begin{center}
<<IrisDataPlot1,fig.width=10,fig.height=10,out.width='\\textwidth'>>=
plot(apIris1, iris)
@
\end{center}
The heatmap looks as follows:
\begin{center}
<<IrisDataHeatmap1,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(apIris1)
@
\end{center}

Now let us try to obtain fewer clusters by using the minimum of off-diagonal similarities:
<<IrisData2>>=
data(iris)
apIris2 <- apcluster(negDistMat(r=2), iris, q=0)
apIris2
@
AP has identified \Sexpr{length(apIris2)} clusters. If we again superimpose them in
the scatter plot matrix, we obtain the following:
\begin{center}
<<IrisDataPlot,fig.width=10,fig.height=10,out.width='\\textwidth'>>=
plot(apIris2, iris)
@
\end{center}
Finally, the heatmap looks as follows:

\begin{center}
<<IrisDataHeatmap2,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(apIris2)
@
\end{center}
So, looking at the heatmap, the \Sexpr{length(apIris2)} clusters seem quite reasonable,
at least in the light of the fact that there are three species in the data
set, {\em Iris setosa}, {\em Iris versicolor}, and {\em Iris virginica}, where
{\em Iris setosa}
is very clearly separated from each other (first cluster in the heatmap) and the two others
are partly overlapping.

\section{Exemplar-based Agglomerative Clustering}\label{sec:agglo}

The function \verb+aggExCluster()+ realizes what can best be
described as ``exemplar-based agglomerative clustering'', i.e.\
agglomerative clustering whose merging objective is geared towards
the identification of meaningful exemplars.  Analogously to \verb+apcluster()+,
\verb+aggExCluster()+ supports two variants --- it can either be called
for a similarity measure and data or on matrix of pairwise similarities.

\subsection{Getting started}

Let us start with a simple example:
<<AggExClusterDataSet1>>=
aggres1a <- aggExCluster(negDistMat(r=2), x1)
aggres1a
@
The output object \verb+aggres1a+ contains the complete cluster hierarchy.
As obvious from the above example, the \verb+show()+ method only displays
the most basic information. Calling \verb+plot()+ on an object that
was the result of \verb+aggExCluster()+ (an object of class
\verb+AggExResult+), a dendrogram is plotted:
\begin{center}
<<DendrogramAggExClusterDataSet1,fig.width=5,fig.height=5,out.width='0.5\\textwidth'>>=
plot(aggres1a)
@
\end{center}
The heights of the merges in the dendrogram correspond to the merging
objective: the higher the vertical bar of a merge, the less similar the
two clusters have been. The dendrogram, therefore, clearly indicates
two clusters.
Heatmaps can be produced analogously as for \verb+APResult+ objects with the
additional property that dendrograms are displayed on the top and on the left:
\begin{center}
<<HeatmapAggExClusterDataSet1,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(aggres1a, s1)
@
\end{center}

Once we have confirmed the number of clusters, which is clearly 2 according
to the dendrogram and the heatmap above, we can extract the level with
two clusters from the cluster hierarchy. In concordance with standard
\R\ terminology, the function for doing this is called \verb+cutree()+:
\begin{center}
<<ExtractAggExClustersDataSet1,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
cl1a <- cutree(aggres1a, k=2)
cl1a
plot(cl1a, x1)
@
\end{center}

\subsection{Merging clusters obtained from affinity propagation}

The most important application of \verb+aggExCluster()+ (and the reason
why it is part of the \APCluster\ package) is that it can be used
for creating a hierarchy of clusters starting from a set of clusters
previously computed by affinity propagation. The examples in Section
\ref{sec:ipref} indicate that it may sometimes be tricky to define the
right input preference. Exemplar-based agglomerative clustering on
affinity propagation results provides an additional tool for finding the
right number of clusters.

Let us revisit the four-cluster example from Section
\ref{sec:ipref}. We can apply \verb+aggExCluster()+ to an affinity
propagation result if we run it on the affinity propagation result supplied
as second argument \verb+x+:
<<AggExClusterAPDataSet2q08>>=
aggres2a <- aggExCluster(x=apres2c)
aggres2a
@
The result \verb+apres2c+ had \Sexpr{length(apres2c)} clusters.
\verb+aggExCluster()+ successively joins these clusters until only one
cluster is left. The dendrogram of this cluster hierarchy is given as
follows:
\begin{center}
<<DendrogramAggExAPDataSet2,fig.width=5,fig.height=5,out.width='0.5\\textwidth'>>=
plot(aggres2a)
@
\end{center}
If one wants to see the original samples in the dendrogram of the cluster hierarchy,
the \verb+showSamples=TRUE+ option can be used. In this case, it is recommended to
reduce the font size of
the labels via the \verb+nodePar+ parameter (see \verb+?plot.dendrogram+ and the examples
therein):
\begin{center}
<<DendrogramAggExAPDataSet2b,fig.width=5,fig.height=5,out.width='0.5\\textwidth'>>=
plot(aggres2a, showSamples=TRUE, nodePar=list(pch=NA, lab.cex=0.4))
@
\end{center}

The following heatmap coincides with the one shown in Section \ref{sec:ipref}
above. This is not surprising, since the heatmap plot for an affinity
propagation result uses \verb+aggExCluster()+ internally to arrange
the clusters:
\begin{center}
<<HeatmapAggExAPDataSet2,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(aggres2a)
@
\end{center}

Once we are more or less sure about the number of clusters, we extract
the right clustering level from the hierarchy. For demonstation purposes,
we do this for $k=5,\dots,2$ in the following plots:
\begin{center}
<<PlotAggExAPDataSet2k25,fig.width=8,fig.height=8,out.width='\\textwidth'>>=
par(mfrow=c(2,2))
for (k in 5:2)
    plot(aggres2a, x2, k=k, main=paste(k, "clusters"))
@
\end{center}

There is one obvious, but important, condition: applying
\verb+aggExCluster()+ to an affinity propagation result only makes sense
if the number of clusters to start from is at least as large as the
number of true clusters in the data set. Clearly, if the number of clusters
is already too small, then merging will make the situation only worse.


\subsection{Details on the merging objective}

Like any other agglomerative clustering method (see, e.g.,
\cite{JainMurtyFlynn99,MichalskiStepp92,Ward63}),
\verb+aggExCluster()+ merges clusters until only one cluster containing
all samples is obtained. In each step, two clusters are merged into one,
i.e.\ the number of clusters is reduced by one. The only aspect in which
\verb+aggExCluster()+ differs from other methods
is the merging objective.

Suppose we consider two clusters for possible merging,
each of which is given by an index set:
\[
  I = \{i_1,\dots,i_{n_I}\} \text{ and } J = \{j_1,\dots,j_{n_J}\}
\]
Then we first determine the potential
{\em joint exemplar} $\mathop{\mathrm{ex}}(I,J)$ as the sample that
maximizes the average similarity
to all samples in the joint cluster $I\cup J$:
\[
\mathop{\mathrm{ex}}(I,J) =\mathop{\mathrm{argmax}}\limits_{i\in I\cup J}
\frac{1}{n_I + n_J}\cdot \sum\limits_{j\in I\cup J} S_{ij}
\]
Recall that $\mathbf{S}$ denotes the similarity matrix and $S_{ij}$
corresponds to the similarity of the $i$-th and the $j$-th sample.
Then the merging objective is computed as
\[
\mathop{\mathrm{obj}}(I,J)=\frac{1}{2}\cdot\Big(\frac{1}{n_I}\cdot
\sum\limits_{j\in I} S_{\mathop{\mathrm{ex}}(I,J)j}+\frac{1}{n_J}\cdot
\sum\limits_{k\in J} S_{\mathop{\mathrm{ex}}(I,J)k}\Big),
\]
which can be best described as ``{\em balanced average similarity to the joint
exemplar}''. In each step, \verb+aggExCluster()+ considers all pairs
of clusters in the current cluster set and joins that pair of clusters whose
merging objective is maximal. The rationale behind the merging objective is
that those two clusters should be joined that are best described by a joint
exemplar.

\section{Leveraged Affinity Propagation}\label{sec:lever}

Leveraged affinity propagation is based on the idea that, for large data sets
with many samples, the cluster structure is already visible on a subset
of the samples. Instead of evaluating the similarity matrix for all sample
pairs, the similarities of all samples to a subset of samples are computed ---
resulting in a non-square similarity matrix. Clustering is performed on this
reduced similarity matrix allowing for clustering large data sets more
efficiently.

In this form of clustering, several rounds of affinity propagation are
executed with different sample subsets --- iteratively improving the clustering
result. The implementation is based on the Matlab code of Frey and Dueck
provided on the AP Web page\footnotemark[1]. Apart from dynamic
improvements through reduced amount of distance calculations and faster
clustering, the memory consumption is also reduced not only in terms of the
memory used for storing the similarity matrix, but also in terms of
memory used by the clustering algorithm internally.

The two main parameters controlling leveraged AP clustering are the fraction
of data points that should be selected for clustering (parameter \verb+frac+)
and the number of sweeps or repetitions of individual clustering runs
(parameter \verb+sweeps+).
Initially, a sample subset is selected randomly. For the subsequent
repetitions, the exemplars of the previous run are kept in the sample subset
and the other samples in the subset are chosen randomly again. The best
result  of all sweeps with the highest net similarity is kept as final
clustering result.

When called with a similarity measure and a dataset the function
\verb+apclusterL()+ performs both the calculation of similarities and
leveraged affinity propagation. In the example below, we use  10\% of the
samples and run 5 repetitions. The function implementing
the similarity measure can either be passed as a function or as a function
name (which must of course be resolvable in the current environment).
Additional parameters for the distance calculation can be passed to
\verb+apclusterL()+ which passes them on to the function implementing
the similarity measure via the \verb+...+ argument list. In any case, this
function must be implemented such that it expects the data in its first argument
\verb+x+ (a subsettable data structure, such as, a vector, matrix, data frame,
or list) and that it takes the selection of ``column objects'' as a second
argument \verb+sel+ which must be a set of column indices.
The functions \verb+negDistMat()+, \verb+expSimMat()+, \verb+linSimMat()+,
\verb+corSimMat()+, and \verb+linKernel()+ provided by the
\APCluster\ package also support the easy creation of parameter-free
similarity measures (in R terminology called ``closures''). We recommend
this variant, as it is safer in terms of possible name conflicts between
arguments of \verb+apclusterL()+ and arguments of the similarity function.

Here is an example that makes use of a closure for defining the similarity
measure:
\begin{center}
<<APClusterLevDataSet3,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
cl5 <- cbind(rnorm(100, 0.3, 0.05), rnorm(100, 0.7, 0.04))
cl6 <- cbind(rnorm(100, 0.70, 0.04), rnorm(100, 0.4, 0.05))
x3 <- rbind(cl5, cl6)
apres3 <- apclusterL(s=negDistMat(r=2), x=x3, frac=0.1, sweeps=5, p=-0.2)
apres3
plot(apres3, x3)
@
\end{center}

The function \verb+apclusterL()+ creates a result object of S4 class
\verb+APResult+ that contains the same information as for standard AP.
Additionally, the selected sample subset, the associated rectangular
similarity matrix for the best sweep (provided that \verb+includeSim=TRUE+)
and the net similarities of all sweeps are returned in this object.
<<APClusterLevResultDataSet3>>=
dim(apres3@sim)
apres3@sel
apres3@netsimLev
@
The result returned by leveraged affinity propagation can be used for
further processing in the same way as a result object returned from
\verb+apcluster()+, e.g., merging of clusters with agglomerative
clustering can be performed.

For heatmap plotting either the parameter \verb+includeSim=TRUE+ must be set
in \verb+apcluster()+ or \verb+apclusterL()+ to make the similarity matrix
available in the result object or the similarity matrix must be passed as
second parameter to \verb+heatmap()+ explicitly. The heatmap for
leveraged AP looks slightly different compared to the heatmap for
affinity propagation because the number of samples is different in both
dimensions.

\begin{center}
<<APClusterLevDataSet3Heat,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(apres3)
@
\end{center}

Often selected samples will be chosen as exemplars because, only for
them, the full similarity information is available. This means that the
fraction of samples should be selected in a way such that a
considerable number of samples is available for each expected cluster.
Please also note that a data set of the size used in this example can
easily be clustered with regular affinity propagation. The data set was
kept small to keep the package build time short and the amount of
data output in the manual reasonable.

For users requiring a higher degree of flexibility, e.g., for
a customized selection of the sample subset,
\verb+apclusterL()+ called with a rectangular similiarity matrix performs
affinity propagation on a rectangular similarity
matrix. See the source code of \verb+apclusterL()+ with signature
\verb+s=function+ and \verb+x=ANY+ for an example how to
embed \verb+apclusterL()+ into a complete loop performing leveraged AP.
The package-provided functions for distance calculation support the
generation of rectangular similarity matrices (see Chapter \ref{sec:DistMat}).

\section{Sparse Affinity Propagation}\label{sec:sparse}

Starting with Version 1.4.0 of the \APCluster\ package, the functions \verb+apcluster()+,
\verb+apclusterK()+, and \verb+preferenceRange()+ can also handle similarity matrices as
defined by the \verb+Matrix+ package. While all dense matrix formats are converted to standard
R matrices, sparse matrices are converted internally to \verb+dgTMatrix+ objects.
For these sparse matrices, special implementations of the \verb+apcluster()+,
\verb+apclusterK()+, and \verb+preferenceRange()+ are available that fully exploit the
sparseness of the matrices and may require much less operations if the matrix is
sufficiently sparse.

In order to demonstrate that, consider the following example:
<<SparseEx1>>=
dsim <- negDistMat(x2, r=2)
ssim <- as.SparseSimilarityMatrix(dsim, lower=-0.2)
str(ssim)
@
The function \verb+as.SparseSimilarityMatrix()+ converts the dense similarity matrix
\verb+dsim+ into a sparse similarity matrix by removing all pairwise similarities that
are -0.2 or lower. Note that this is only for demonstration purposes. If the size of
data permits that, it is advisable to use the entire dense similarity matrix. Anyway,
let us run sparse AP on this similarity matrix:
\begin{center}
<<SparseEx1Run,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
sapres <- apcluster(ssim, q=0)
plot(sapres, x2)
@
\end{center}

The functions \verb+preferenceRange()+ and \verb+apclusterK()+ work in the same way as for
dense similarity matrices:
<<SparseEx1Run2>>=
preferenceRange(ssim)
apclusterK(ssim, K=2)
@

The functions \verb+aggExCluster()+ and \verb+heatmap()+ have been extended to be able
to handle sparse matrices. Note, however, that these functions are not yet exploiting
sparsity properly. Instead, they convert all inputs to dense matrices before processing
them, which may lead to memory and/or performance issues for large data sets.
\begin{center}
<<SparseEx1RunHeatmap,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(sapres, ssim)
@
\end{center}
The above heatmap illustrates that values that are not stored in the sparse similarity matrix
are filled up with low values (see the red areas between some pairs of samples that belong
to different clusters). Actually, each missing value is replaced with
\[
\min(s)-(\max(s)-\min(s))=2\cdot\min(s)-\max(s),
\]
where $\min(s)$ and $\max(s)$ denote the smallest and the largest similarity value specified
in the sparse similarity matrix $s$, respectively. The same replacement takes place when
\verb+aggExCluster()+ converts sparse similarity matrices to dense ones.


\section{A Toy Example with Biological Sequences}\label{sec:bioseq}

As noted in the introduction above, one of the goals of this package is
to leverage affinity propagation in bioinformatics applications.
In order to demonstrate the usage of the package in a biological application,
we consider a small toy example here.

The package comes with a toy data set \verb+ch22Promoters+ that consists of
sub-sequences of promoter regions of 150 random genes from the human
chromosome no.\ 22
(according to the human genome assembly hg18). Each sequence
consists of the 1000 bases upstream of the transcription start site of each
gene. Suppose we want to cluster these sequences in order to find out whether
groups of promoters can be identified on the basis of the sequence only and,
if so, to identify exemplars that are most typical for these groups.
<<LoadCh22Promoters>>=
library(Biostrings)
filepath <- system.file("examples", "ch22Promoters.fasta",
                        package="apcluster")
ch22Promoters <- readDNAStringSet(filepath)
ch22Promoters
@
Obviously, these are classical nucleotide sequences, each of which is identified
by the RefSeq identifier of the gene the promoter sequence stems from.

In order to compute a similarity matrix for this data set, we choose
(without further justification, just for demonstration purposes) the
simple {\em spectrum kernel} \cite{LeslieEskinNoble02} with a sub-sequence
length of $k=6$. We use the implementation from the \KeBABS\ package
\cite{PalmeHochreiterBodenhofer15} to
compute the similarity matrix in a convenient way:
<<SimCh22Promoters>>=
library(kebabs)
specK6 <- spectrumKernel(k=6)
promSim <- getKernelMatrix(specK6, ch22Promoters)
promSim[1:4, 1:4]
@
Now we run affinity propagation on the similarity matrix:
<<APCh22Promoters>>=
promAP <- apcluster(promSim, q=0)
promAP
@
So we obtain \Sexpr{length(promAP@exemplars)} clusters in total. The
corresponding heatmap looks as follows (note that we have to supply the
similarity matrix, as it is not included by default if \verb+apcluster()+
is called with the similarity matrix; the reason is that, for large
data sets, it is more memory-efficient not to make multiple copies of the
similarity matrix; see also \ref{ssec:memeff}):
\begin{center}
<<HeatMapAPCh22Promoters,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(promAP, promSim, Rowv=FALSE, Colv=FALSE)
@
\end{center}
Let us now run agglomerative clustering to further join clusters.
<<aggExCh22Promoters>>=
promAgg <- aggExCluster(promSim, promAP)
@
The resulting dendrogram is given as follows:
\begin{center}
<<DendrogramAPCh22Promoters,fig.width=5,fig.height=5,out.width='0.5\\textwidth'>>=
plot(promAgg)
@
\end{center}
The dendrogram does not give a very clear indication about the best number of
clusters. Let us adopt the viewpoint for a moment that 5 clusters are
reasonable.
<<ExtractAggCh22Promoters>>=
prom5 <- cutree(promAgg, k=5)
prom5
@
The final heatmap looks as follows:
\begin{center}
<<HeatMap5Ch22Promoters,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(prom5, promSim, Rowv=FALSE, Colv=FALSE)
@
\end{center}

\section{Similarity Matrices}\label{sec:DistMat}

Apart from the obvious monotonicity ``the higher the value, the more similar
two samples'', affinity propagation does not make any specific assumption about
the similarity measure. Negative squared distances must be used if one wants
to minimize squared errors \cite{FreyDueck07}. Apart from that, the choice and
implementation of the similarity measure is left to the user.

Our package offers a few more methods to obtain similarity matrices.
The choice of the right one (and, consequently, the objective function the
algorithm optimizes) still has to be made by the user.

All functions described in this section assume the input data matrix to be
organized such that each row corresponds to one sample and each column
corresponds to one feature (in line with the standard function \verb+dist+).
If a vector is supplied instead of a matrix, each single entry is interpreted as
a (one-dimensional) sample.

\subsection{The function \texttt{negDistMat()}}

The function \verb+negDistMat()+, in line with Frey and Dueck, allows for
computing negative distances for a given set of real-valued data samples.
If called with the first argument \verb+x+, a similarity matrix with
pairwise negative distances is returned:
<<NegDistMatDataSet2>>=
s <- negDistMat(x2)
@
The function \texttt{negDistMat()} provides the same set of distance measures
and parameters as the standard function \verb+dist()+
(except for \verb+method="binary"+ which makes little sense for
real-valued data).
Presently, \verb+negDistMat()+ provides the following
variants of computing the distance $d(\vec{x},\vec{y})$ of two data samples
$\vec{x}=(x_1,\dots,x_n)$ and $\vec{y}=(y_1,\dots,y_n)$:
\begin{description}
\item[Euclidean:]
\[
d(\vec{x},\vec{y})=\sqrt{\sum\limits_{i=1}^n (x_i-y_i)^2}
\]
use \verb+method="euclidean"+ or do not specify argument \verb+method+
(since this is the default);
\item[Maximum:]
\[
d(\vec{x},\vec{y})=\max\limits_{i=1}^n |x_i-y_i|
\]
use \verb+method="maximum"+;
\item[Sum of absolute distances / Manhattan:]
\[
d(\vec{x},\vec{y})=\sum\limits_{i=1}^n |x_i-y_i|
\]
use \verb+method="manhattan"+;
\item[Canberra:]
\[
d(\vec{x},\vec{y})=\sum\limits_{i=1}^n \frac{|x_i-y_i|}{|x_i+y_i|}
\]
summands with zero denominators are not taken into account;
use \verb+method="canberra"+;
\item[Minkowski:]
\[
d(\vec{x},\vec{y})=\left(\sum\limits_{i=1}^n (x_i-y_i)^p\right)^{\frac{1}{p}}
\]
use \verb+method="minkowski"+ and specify $p$ using the additional argument
$\verb+p+$ (default is \verb+p=2+, resulting in the standard Euclidean
distance);
\item[Discrepancy:]
\[
d(\vec{x},\vec{y})=\max\limits_{1\leq\alpha\leq\beta\leq n}\left|\sum\limits_{i=\alpha}^{\beta} (y_i-x_i)\right|
\]
use \verb+method="discrepancy"+ \cite{Weyl16}.
\end{description}

The function \verb+negDistMat()+ then takes the distances computed with one of the
variants listed above and returns $-1$ times the $r$-th power of it, i.e.,
\begin{equation}\label{eq:negDistMat}
s(\vec{x},\vec{y})=-d(\vec{x},\vec{y})^r.
\end{equation}
The exponent $r$ can be adjusted with the argument \verb+r+. The default is
\verb+r=1+, hence, one has to supply \verb+r=2+ to
obtain negative squared distances as in the examples in previous sections.

Here are some examples:
<<CreateToyData>>=
ex <- matrix(c(0, 0.5, 0.8, 1, 0, 0.2, 0.5, 0.7,
               0.1, 0, 1, 0.3, 1, 0.8, 0.2), 5, 3, byrow=TRUE)
ex
@
Standard Euclidean distance:
<<NegEuclDistMatToyData>>=
negDistMat(ex)
@
Squared Euclidean distance:
<<NegSqEuclDistMatToyData>>=
negDistMat(ex, r=2)
@
Maximum norm-based distance:
<<NegMaxDistToyData>>=
negDistMat(ex, method="maximum")
@
Sum of absolute distances (aka Manhattan distance):
<<NegManhattanDistToyData>>=
negDistMat(ex, method="manhattan")
@
Canberra distance:
<<NegCanberraDistToyData>>=
negDistMat(ex, method="canberra")
@
Minkowski distance for $p=3$ ($3$-norm):
<<NegMinkowskiDistToyData>>=
negDistMat(ex, method="minkowski", p=3)
@

If called without the data argument \verb+x+, a function object is returned that
can be supplied to clustering functions --- as in the majority of the above
examples:
<<GetFunction>>=
sim <- negDistMat(r=2)
is.function(sim)
apcluster(sim, x1)
@

Depending on the application, it might be advisable to center and/or scale the
data in order to equalize the influence of all features/columns. This makes
sense for standard vector space distances like the Euclidean distance and can
easily be accomplished by the \verb+scale()+ method. The discrepancy distance,
in contrast, is strongly dependent on the order to feature/columns and is rather
aimed at comparing signals. For this measure, therefore, row-wise centering can
be advisable \cite{BauerBodenhoferKlement96c}. This is easily done with the
\verb+sweep()+ function:
<<DiscrepancyDistToyData,fig.width=6,fig.height=4.5,out.width='0.6\\textwidth'>>=
ex2 <- matrix(c(0, 0, 1, 1, 1, 0, 0, 0,
                0, 0, 0, 0, 0, 1, 1, 0,
                0, 1, 0, 1, 0, 1, 0, 1), 3, 8, byrow=TRUE)

matplot(t(ex2), ylab="")
matlines(t(ex2), type="s")

negDistMat(ex2, method="discrepancy")

ex2Scaled <- sweep(ex2, 1, rowMeans(ex2))
ex2Scaled

matplot(t(ex2Scaled), ylab="")
matlines(t(ex2Scaled), type="s")

negDistMat(ex2Scaled, method="discrepancy")
@

\subsection{Other similarity measures}

The package \APCluster\ offers four more functions for creating similarity
matrices for real-valued data:

\begin{description}
\item[Exponential transformation of distances:] the function \verb+expSimMat()+
works in the same way as the function \verb+negDistMat()+. The difference is
that, instead of the transformation \eqref{eq:negDistMat}, it uses the
following transformation:
\[
s(\vec{x},\vec{y})=\exp\left(-\left(\frac{d(\vec{x},\vec{y})}{w}\right)^r\right)
\]
Here the default is \verb+r=2+. It is clear that \verb+r=2+ in conjunction with
\verb+method="euclidean"+ results in the well-known
{\em Gaussian kernel / RBF kernel}
\cite{FitzGeraldMicchelliPinkus95,Micchelli86,SchoelkopfSmola02}, whereas
\verb+r=1+ in conjunction with
\verb+method="euclidean"+ results in the similarity measure that is sometimes
called {\em Laplace kernel} \cite{FitzGeraldMicchelliPinkus95,Micchelli86}.
Both variants (for non-Euclidean distances as well) can also be interpreted
as {\em fuzzy equality/similarity relations}
\cite{DeBaetsMesiar02}.
\item[Linear scaling of distances with truncation:]
the function \verb+linSimMat()+ uses the transformation
\[
s(\vec{x},\vec{y})=\max\left(1-\frac{d(\vec{x},\vec{y})}{w},0\right)
\]
which is also often interpreted as a {\em fuzzy equality/similarity relation}
\cite{DeBaetsMesiar02}.
\item[Correlation:]
the function \verb+corSimMat()+ interprets the rows of its
argument \verb+x+ (matrix or data frame) as multivariate observations and
computes similarities as pairwise correlations. The function
\verb+corSimMat()+ is actually a wrapper around the standard function
\verb+cor()+. Consequently, the \verb+method+ argument allows for selecting
the type of correlation to compute (Pearson, Spearman, or Kendall).
\item[Linear kernel:] scalar products can also be interpreted as similarity
measures, a view that is often adopted by kernel methods in machine learning.
In order to provide the user with this option as well, the function
\verb+linKernel()+ is available. For two data samples
$\vec{x}=(x_1,\dots,x_n)$ and
$\vec{y}=(y_1,\dots,y_n)$, it computes the similarity as
\[
s(\vec{x},\vec{y})=\sum\limits_{i=1}^n x_i\cdot y_i.
\]
The function has one additional argument, \verb+normalize+ (default:
\verb+FALSE+). If \verb+normalize+ is set to \verb+TRUE+, values are
normalized to the range $[-1,+1]$ in the following way:
\[
s(\vec{x},\vec{y})=\frac{\sum_{i=1}^n x_i\cdot y_i}%
{\sqrt{\big(\sum_{i=1}^n x_i^2\big)\cdot%
\big(\sum_{i=1}^n y_i^2\big)}}
\]
Entries for which at least one of the two factors in the denominator
is zero are set to zero (however, the user should be aware that this
should be avoided anyway).
\end{description}

For the same example data as above, we obtain the
following for the RBF kernel:
<<RBFKernelToyData>>=
expSimMat(ex)
@
Laplace kernel:
<<LaplaceKernelToyData>>=
expSimMat(ex, r=1)
@
Pearson correlation coefficient:
<<PearsonToyData>>=
corSimMat(ex, method="pearson")
@
Spearman rank correlation coefficient:
<<SpearmanToyData>>=
corSimMat(ex, method="spearman")
@
Linear scaling of distances with truncation:
<<TruncDistToyData>>=
linSimMat(ex, w=1.2)
@
Linear kernel:
<<LinKernelToyData>>=
linKernel(ex[2:5,])
@
Normalized linear kernel:
<<NormLinKernelToyData>>=
linKernel(ex[2:5,], normalize=TRUE)
@

All of these functions work in the same way as \verb+negDistMat()+: if called
with argument \verb+x+, a similarity matrix is returned, otherwise a
function is returned.

\subsection{Rectangular similarity matrices}

With the introduction of leveraged affinity propagation, distance
calculations are entirely performed within the \APCluster\ package. The code is
based on a customized version of the \verb+dist()+ function from the
\verb+stats+ package. In the following example, a rectangular similarity
matrix of all samples against a subset of the samples is computed:
<<RectangularNegDistMatDataSet1>>=
sel <- sort(sample(1:nrow(x1), ceiling(0.08 * nrow(x1))))
sel
s1r <- negDistMat(x1, sel, r=2)
dim(s1r)
s1r[1:7,]
@

The rows correspond to all samples, the columns to the sample subset.
The \verb+sel+ parameter specifies the sample indices of the selected samples in
increasing order. Rectangular similarity calculation is provided in all distance
functions of the package. If the parameter \verb+sel+ is not specified,
the quadratic similarity matrix of all sample pairs is computed.

\subsection{Defining a custom similarity measure for leveraged affinity
  propagation}\label{ssec:leverSim}

As mentioned in Section \ref{sec:lever} above, leveraged affinity propagation
requires the definition of a similarity measure that is supplied as a
function or function name to \verb+apclusterL()+. For vectorial data,
the similarity measures supplied with the package (see above) may be
sufficient. If other similarity measures are necessary or if the data
are not vectorial, the user must supply his/her own similarity measure.
The user can supply any function as argument \verb+s+ to
\verb+apcluster()+, \verb+apclusterK()+, or \verb+apclusterL()+, but the
following rules must be obeyed in order to avoid errors and to ensure meaningful results:
\begin{enumerate}
\item The data must be supplied as first argument, which must be named
  \verb+x+.
\item The second argument must be named \verb+sel+ and must be interpreted as a
  vector of indices that select a subset of data items in \verb+x+.
\item The function must return a numeric matrix with similarities.
  If \verb+sel=NA+, the format of the matrix must be
  \verb+length(x)+$\times$\verb+length(x)+. If \verb+sel+ is not \verb+NA+,
  but contains indices selecting a subset, the format of the returned
  similarity matrix must be  \verb+length(x)+$\times$\verb+length(sel)+.
\item Although this is not a must, it is recommended to properly set
  row and column names in the returned similarity matrix.
\end{enumerate}

As an example, let us revisit the sequence clustering example presented
in Section \ref{sec:bioseq}. Let us first define the function that implements
the similarity measure:
<<SimFunCh22Promoters>>=
spectrumK6 <- function(x, sel=NA)
{
    if (any(is.na(sel)))
        s <- getKernelMatrix(specK6, x)
    else
        s <- getKernelMatrix(specK6, x, x[sel])

    as(s, "matrix")
}
@
Now we run leveraged affinity propagation on the \verb+ch22Promoters+
data set using this similarity measure
<<APCh22Promoters2>>=
promAPL <- apclusterL(s=spectrumK6, ch22Promoters, frac=0.1, sweeps=10,
                      p=promAP@p)
promAPL
@
So we obtain \Sexpr{length(promAPL@exemplars)} clusters in total.

\subsection{Defining a custom similarity measure that creates a sparse similarity matrix}

Since Version 1.4.0, similarity matrices may also be sparse (cf.~Section~\ref{sec:sparse}).
Correspondingly, the similarity measures passed to \verb+apcluster()+ and \verb+apclusterK()+
may also return sparse similarity matrices:
<<CustomSimSparse>>=
sparseSim <- function(x)
{
    as.SparseSimilarityMatrix(negDistMat(x, r=2), lower=-0.2)
}

sapres2 <- apcluster(sparseSim, x2, q=0)
sapres2
str(similarity(sapres2))
@
Note that similarity measures passed to \verb+apclusterL()+ may not return sparse matrices.
Instead, they must accept a \verb+sel+ argument and return a rectangular dense matrix
(see Subsection~\ref{ssec:leverSim} above).

\section{Miscellaneous}

\subsection{Convenience vs.\ efficiency}\label{ssec:memeff}

In most of the above examples, we called a clustering method by supplying
it with a similarity function and the data to be clustered. This is undoubtedly
a convenient approach. Since the resulting output objects (unless
the option \verb+includeSim=FALSE+ is supplied) even includes the
similarity matrix, we can plot heatmaps and produce a
cluster hierarchy on the basis of the clustering result without the need to
supply the similarity matrix explicitly.

For large data sets, however, this convenient approach has some disadvantages:
\begin{itemize}
\item If the clustering algorithm is run several times on the same data set
(e.g., for different parameters), the similarity matrix is recomputed every
time.
\item Every clustering result (depending on the option \verb+includeSim+)
usually includes a copy of the similarity matrix.
\end{itemize}
For these reasons, depending on the actual application scenario, users
should consider computing the similarity matrix beforehand. This strategy,
however, requires some extra effort for subsequent processing, i.e.\ the
similarity must be supplied as an extra argument in subsequent processing.

\subsection{Clustering named objects}\label{ssec:names}

The function \verb+apcluster()+ and all functions for computing distance
matrices are implemented to recognize names of data objects and to correctly
pass them through computations. The mechanism is best described with a simple
example:
<<CreateLabeledToyData>>=
x3 <- c(1, 2, 3, 7, 8, 9)
names(x3) <- c("a", "b", "c", "d", "e", "f")
s3 <- negDistMat(x3, r=2)
@
So we see that the \verb+names+ attribute must be used if a vector of
named one-dimensional samples is to be clustered. If the data are not
one-dimensional (a matrix or data frame), object names must be stored in the row
names of the data matrix.

All functions for computing similarity matrices recognize the object names. The
resulting similarity matrix has the list of names both as row and column names.
<<ShowToyDataLabels>>=
s3
colnames(s3)
@
The function \verb+apcluster()+ and all related functions use column names
of similarity matrices as object names. If object names are available,
clustering results are by default shown by names.
<<ClusterLabeledToyData>>=
apres3a <-apcluster(s3)
apres3a
apres3a@exemplars
apres3a@clusters
@

\subsection{Computing a label vector from a clustering result}
\label{ssec:labels}

For later classification or comparisons with other clustering methods, it
may be useful to compute a label vector from a clustering result. Our package
provides an instance of the generic function \verb+labels()+ for this task. As
obvious from the following example, the argument \verb+type+ can be used to
determine how to compute the label vector.
<<ExtractLabelsFromClusterToyData>>=
apres3a@exemplars
labels(apres3a, type="names")
labels(apres3a, type="exemplars")
labels(apres3a, type="enum")
@
The first choice, \verb+"names"+ (default), uses names of exemplars as labels
(if names are available, otherwise an error message is displayed). The second
choice, \verb+"exemplars"+, uses indices of exemplars (enumerated as in the
original data set). The third choice, \verb+"enum"+, uses indices of clusters
(consecutively numbered as stored in the slot \verb+clusters+ --- analogous
to the standard implementation of \verb+cutree()+ or the
\verb+clusters+ field of the list returned by the standard function
\verb+kmeans()+).

\subsection{Customizing heatmaps}

With Version 1.3.1, the implementation of heatmap plotting has changed significantly.
The method now allows for many more customizations than before.
Apart from changes in the argument list (see \verb+?heatmap+), the behavior
of the method has changed as follows:
\begin{itemize}
  \item Dendrograms are always plotted if possible. To switch off plotting
    of dendrograms, set \verb+Rowv+ and \verb+Colv+ to \verb+FALSE+ or \verb+NA+.
    If a dendrogram should only appear to the left of the heatmap, set
    \verb+Colv+ to \verb+FALSE+ or \verb+NA+. Analogously, set \verb+Rowv+ to
    \verb+FALSE+ or \verb+NA+ if a dendrogram should only be plotted on top of the
    plot (not possible if the similarity matrix is non-quadratic).
  \item Previously, \verb+rainbow()+ was used internally to determine how the
    bars illustrating the clusters are colored. Now users can determine the coloring
    of the color bars using the \verb+sideColors+ argument. For \verb+sideColors=NULL+,
    a meaningful color coding is determined automatically which still uses  \verb+rainbow()+,
    but ensures that no similar colors are placed next to each other in the bar.
  \item The default font sizes for displaying row/column labels have been changed to
    make sure that they do not overlap. This can result in quite small labels if the
    number of samples is larger. In any case, the user can override the sizes by making
    custom settings of the parameters \verb+cexRow+ and \verb+cexCol+. Row and column
    labels can even be switched off
    entirely by setting \verb+cexRow+ and \verb+cexCol+ to 0, respectively.
\end{itemize}
Moreover, with Version~1.4.3, the possibility to add a color legend has been integrated.

Here is an example with the vertical dendrogram switched off, an alternate color scheme,
custom margins, and a color legend:
\begin{center}
<<HeatmapResultAPClusterDataSetq08b,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(apres2c, sideColors=c("darkgreen", "yellowgreen"),
        col=terrain.colors(12), Rowv=FALSE, dendScale=0.5,
        margins=c(3, 3, 2), legend="col")
@
\end{center}

The following example reverts to the default behavior prior to Version 1.3.1: consecutive
rainbow colors, no dendrograms, and traditional sizing of row/column labels:
\begin{center}
<<HeatmapResultAPClusterDataSet2q08c,fig.width=7,fig.height=7,out.width='0.6\\textwidth'>>=
heatmap(apres2c, sideColors=rainbow(length(apres2c)), Rowv=FALSE, Colv=FALSE,
        cexRow=(0.2 + 1 / log10(nrow(apres2c@sim))),
        cexCol=(0.2 + 1 / log10(nrow(apres2c@sim))))
@
\end{center}

\subsection{Adding a legend to plots of clustering results}

As shown above, \verb+plot()+ called for an \verb+APResult+ object as first and a
matrix or data frame as second argument plots the clustering result superimposed on
a scatter plot (or a scatter plot matrix if the number of columns in the second argument
exceeds 2). The clusters are shown in different colors, but it may not be clear which
cluster is shown in which color. Therefore, it may be useful to show a legend along
with the plot. The current implementation of \verb+plot()+ does not show a legend, since
it is hard to determine where to actually place the legend such that no important
cluster information gets occluded by the legend. Therefore, the user has to add legends
manually. Actually, colors are always chosen according to a simple rule: \verb+plot()+
uses \verb+rainbow()+ to create a vector of colors that is exactly as long as the
number of clusters in the \verb+APResult+ object. The following example shows how to
plot a legend manually (with the clusters enumerated in the same way as in the \verb+APResult+
object):
\begin{center}
<<PlotAddLegend,fig.width=5,fig.height=5.5,out.width='0.5\\textwidth'>>=
plot(apres2a, x2)
legend("bottomleft", legend=paste("Cluster", 1:length(apres2a)),
       col=rainbow(length(apres2a)), pch=19)
@
\end{center}
Note that this method is only meaningful for plotting clustering results superimposed
on a 2D data set. For scatter plot matrices, this does not work in a meaningful way.
In such a case, the user is rather recommended to create a legend separately
(in a separate graphics device/file) and to display it along with the scatter plot matrix.
To create only the legend, code like the following could be used:
\begin{center}
<<PlotOnlyLegend,fig.width=5,fig.height=2.5,out.width='0.5\\textwidth'>>=
plot.new()
par(oma=rep(0, 4), mar=rep(0, 4))
legend("center", legend=paste("Cluster", 1:length(apres2c)),
       col=rainbow(length(apres2c)), pch=19)
@
\end{center}
It still may be necessary to strip off white margins for further usage of the legend.

\subsection{Implementation and performance issues}\label{ssec:perf}

Prior to Version 1.2.0, \verb+apcluster()+ was implemented in R. Starting with
version 1.2.0, the main iteration loop of  \verb+apcluster()+ has been
implemented in C++ using the Rcpp package  \cite{EddelbuettelFrancois11},
which has led to a speedup in the range of a factor or 9--10.

Note that \verb+details=TRUE+ requires quite an amount of additional memory.
If possible, avoid this for larger data sets.

The asymptotic computational complexity of \verb+aggExCluster()+ is
$\mathcal{O}(l^3)$ (where $l$ is the number of samples or clusters from which
the clustering starts). This may result in excessively long
computation times if \verb+aggExCluster()+ is used for larger data sets
without using affinity propagation first.
For real-world data sets, in particular,
if they are large, we recommend to use affinity propagation first and then,
if necessary, to use \verb+aggExCluster()+ to create a cluster hierarchy.

\subsection{Using APCluster in Conjunction with KeBABS}

The example in Section~\ref{sec:bioseq} makes use of the  \KeBABS\ package
\cite{PalmeHochreiterBodenhofer15}. In previous versions, the two packages
defined the \verb+heatmap()+ methods as S4 generics in conflicting ways.
For this reason, the order in which the two packages were loaded mattered,
and the \verb+heatmap()+ methods of the package that was loaded first
was no longer available. This conflict has been resolved with \KeBABS\
development version 1.5.4. The first official release solving this issue was
1.6.0, which was released as part of Bioconductor 3.3 on May 4, 2016.

\section{Special Notes for Users Upgrading from Previous Versions}

\subsection{Upgrading from a version older than 1.3.0}

Version 1.3.0 has brought several fundamental changes to the architecture
of the package. We tried to ensure backward compatibility with previous
versions where possible. However, there are still some caveats the users
should take into account:
\begin{itemize}
\item The functions \verb+apcluster()+, \verb+apclusterK()+, and
  \verb+aggExCluster()+ have been re-im\-ple\-ment\-ed as S4 generics,
  therefore, they do not have a fixed list of arguments anymore.
  For this reason, users are recommended to name all optional parameters.
\item Heatmap plotting has been shifted to the function \verb+heatmap()+
  which has now been defined as an S4 generic method. Previous methods for
  plotting heatmaps using \verb+plot()+ have been partly available in Versions
  1.3.0 and 1.3.1. Since Version 1.3.2, they are no longer available.
\end{itemize}

\subsection{Upgrading to Version 1.3.3 or newer}

Users who upgrade to Version 1.3.3 (or newer) from an older version should be
aware that the package now requires a newer version of Rcpp.
This issue can simply be solved by re-installing Rcpp from CRAN using
\verb+install.packages("Rcpp")+.

\subsection{Upgrading to Version 1.4.0}

The function \verb+sparseToFull()+ has been deprecated. A fully compatible
function \verb+as.DenseSimilarityMatrix()+ is available that replaces
and extends \verb+sparseToFull()+.

\section{Change Log}

\begin{description}
\item[Version 1.4.5:] \hfill
\begin{itemize}
\item 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
\end{itemize}
\item[Version 1.4.4:] \hfill
\begin{itemize}
\item changed dependency to suggested package \verb+kebabs+ to version of
  at least 1.5.4 for improved interoperability
\item bug fix in \verb+as.dendrogram()+ method with signature `\verb+AggExResult+'
\item added discrepancy metric to distance computations and updated
  \verb+src/distanceL.c+ to new version
\item registered C/C++ subroutines
\item minor change in the vignette template
\item moved \verb+NEWS+ to \verb+inst/NEWS+
\item added \verb+inst/COPYRIGHT+
\end{itemize}
\item[Version 1.4.3:] \hfill
\begin{itemize}
\item added optional color legend to heatmap plotting; in line with this
  change, some minor changes to the interface of the \verb+heatmap()+ function
\item corresponding updates of help pages and vignette
\end{itemize}
\item[Version 1.4.2:] \hfill
\begin{itemize}
\item switched sequence kernel example in vignette from \verb+kernlab+ to \KeBABS\ package
\item workaround to ensure that all \verb+apcluster*()+ methods are able to process
  \verb+KernelMatrix+ objects (cf. \KeBABS\ package)
\item replaced data set \verb+ch22Promoters+ by plain text file (FASTA format)
  in \verb+inst/examples+
\item bug fix in the \verb+heatmap()+ method
\item vignette engine changed from Sweave to knitr
\end{itemize}
\item[Version 1.4.1:] \hfill
\begin{itemize}
\item fixes in C++ code of sparse affinity propagation
\end{itemize}
\item[Version 1.4.0:] \hfill
\begin{itemize}
\item added \verb+apcluster()+ method for sparse similarity matrices;
  as a consequence, the package now imports the \verb+Matrix+ package
  and is now also able to handle non-sparse matrix classes
  defined by the \verb+Matrix+ package. Moreover, similarity functions
  supplied to the \verb+apcluster()+ method may now also return any
  matrix type defined by the \verb+Matrix+ package.
\item fix of \verb+apcluster()+ for dense matrices to better support
  \verb+-Inf+ similarities
\item added \verb+apclusterK()+ method for sparse similarity matrices
\item \verb+preferenceRange()+ is now an S4 generic; re-implementation in
  C++ to speed up function; changed handling of \verb+-Inf+ similarities
  for consistency with sparse version.
\item added \verb+preferenceRange()+ methods for sparse matrices and dense
  matrix objects from the \verb+Matrix+ package.
\item new conversion methods implemented for converting dense similarity
  matrices to sparse ones and vice versa; consequently,
  \verb+sparseToFull()+ is marked as deprecated.
\item adaptation of \verb+heatmap()+ function for improved handling of
  \verb+-Inf+ similarities
\item adaptations of signatures of \verb+[+ and \verb+[[+ accessor methods
\item renamed help page of methods for computing similarity matrices
  to `similarities' in order to avoid confusion with the accessor
  method \verb+similarity()+.
\item corresponding updates of help pages and vignette
\end{itemize}
\item[Version 1.3.5:] \hfill
\begin{itemize}
  \item memory access fixes in C++ code called from \verb+apclusterL()+
  \item minor updates of vignette
\end{itemize}
\item[Version 1.3.4:] \hfill
\begin{itemize}
  \item added \verb+sort()+ function to rearrange clusters according to
    sort criterion; note that this is an S3 method (see help
    page for explanation)
  \item improvements and bug fixes of \verb+apclusterL()+ method for
    signature (\verb+s="matrix"+, \verb+x="missing"+)
  \item performance optimizations of \verb+apcluster()+ and \verb+apclusterL()+
  \item plotting of clustering results superimposed in scatter plot
    matrices now also works for `\verb+AggExResult+' objects
  \item improvements of consistency of error and warning messages
  \item according adaptations of documentation and vignette
  \item adapted dependency and linking to Rcpp version 0.11.1
    (to avoid issues on Mac OS)
  \item minor correction of package namespace
\end{itemize}
\item[Version 1.3.3:] \hfill
\begin{itemize}
  \item adapted dependencies and linking to Rcpp version 0.11.0
  \item cleared up package dependencies
\end{itemize}
\item[Version 1.3.2:] \hfill
\begin{itemize}
  \item 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 \verb+plot()+ can be used to
  draw a heatmap has been removed. From now on, \verb+heatmap()+ must always
  be used.
  \item improved \verb+NA+ handling
  \item correction of input check in \verb+apcluster()+ and \verb+apclusterL()+
    (previously, both functions issued a warning whenever argument \verb+p+ had length $> 1$)
  \item corresponding updates and further improvements of help pages and vignette
\end{itemize}
\item[Version 1.3.1:] \hfill
  \begin{itemize}
  \item re-implementation of \verb+heatmap()+ method: dendrograms can now be plotted
  even for \verb+APResult+ and \verb+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 \verb+sideColor+ argument); dendrograms can be
  switched on and off (by \verb+Rowv+ and \verb+Colv+ arguments);
  \item added \verb+as.hclust()+ and \verb+as.dendrogram()+ methods
  \item added new arguments \verb+base+, \verb+showSamples+, and \verb+horiz+to the \verb+plot()+
    method with signature (\verb+x="AggExResult"+, \verb+y="missing"+); moreover, parameters for
    changing the appearance of the height axis are now respected as well
  \item streamlining of methods (redundant definition of inherited methods removed)
  \item various minor improvements of code and documentation
  \end{itemize}
\item[Version 1.3.0:] \hfill
  \begin{itemize}
  \item added Leveraged Affinity Propagation Clustering
  \item re-implementation of main functions as S4 generic methods in order to
    facilitate the convenient internal computation of similarity matrices
  \item for convenience, similarity matrices can be stored as part of clustering
    results
  \item heatmap plotting now done by \verb+heatmap()+ which has been
    defined as S4 generic
  \item extended interface to functions for computing similarity matrices
  \item added function \verb+corSimMat()+
  \item implementation of \verb+length()+ method for classes \verb+APResult+,
    \verb+AggExResult+, and \verb+ExClust+
  \item added accessor function to extract clustering levels from
    \verb+AggExResult+ objects
  \item correction of exemplars returned by \APCluster\ for
    \verb+details=TRUE+ in slot \verb+idxAll+ of returned \verb+APResult+ object
  \item when using data stored in a data frame, categorical
    columns are now explicitly omitted, thereby, avoiding warnings
  \item all clustering methods now store their calls into the result objects
  \item updates and extensions of help pages and vignette
  \end{itemize}
\item[Version 1.2.0:] \hfill
  \begin{itemize}
  \item reimplementation of \verb+apcluster()+ in C++ using the
    Rcpp package \cite{EddelbuettelFrancois11} which reduces
    computation times by a factor of 9-10
  \item obsolete function \verb+apclusterLM()+ removed
  \item updates of help pages and vignette
  \end{itemize}
\item[Version 1.1.1:] \hfill
  \begin{itemize}
  \item updated citation
  \item minor corrections in help pages and vignette
  \end{itemize}
\item[Version 1.1.0:] \hfill
  \begin{itemize}
  \item added exemplar-based agglomerative clustering function
  \verb+aggExCluster()+
  \item added various plotting functions for dendrograms and heatmaps
  \item extended help pages and vignette according to new functionality
  \item added sequence analysis example to vignette along with data set
    \verb+ch22Promoters+
  \item re-organization of variable names in vignette
  \item added option \verb+verbose+ to \verb+apclusterK()+
  \item numerous minor corrections in help pages and vignette
  \end{itemize}
\item[Version 1.0.3:] \hfill
  \begin{itemize}
  \item Makefile in \verb+inst/doc+ eliminated to avoid installation problems
  \item renamed vignette to ``\verb+apcluster.Rnw+''
  \end{itemize}
\item[Version 1.0.2:] \hfill
  \begin{itemize}
  \item replacement of computation of responsibilities
  and availabilities in function \verb+apcluster()+ by pure matrix operations
  (see \ref{ssec:perf} above); traditional implementation \`a la
  Frey and Dueck still available as function \verb+apclusterLM+;
  \item improved support for named objects (see \ref{ssec:names})
  \item new function for computing label vectors (see \ref{ssec:labels})
  \item re-organization of package source files and help pages
  \end{itemize}
\item[Version 1.0.1:] first official release, released March 2, 2010
\end{description}

\section{How to Cite This Package}

If you use this package for research that is published later, you are kindly
asked to cite it as follows:
\begin{quotation}
\noindent U.\ Bodenhofer, A.\ Kothmeier, and S.\ Hochreiter (2011).
APCluster: an R package for affinity propagation clustering.
{\em Bioinformatics} {\bf 27}(17):2463--2464.
DOI: \href{http://dx.doi.org/10.1093/bioinformatics/btr406}{10.1093/bioinformatics/btr406}.
\end{quotation}
Moreover, we insist that, any time you cite the package, you also cite the
original paper in which affinity propagation has been introduced
\cite{FreyDueck07}.

To obtain Bib\TeX\ entries of the two references, you can enter the following
into your R session:
<<GetBibTeX,eval=FALSE>>=
toBibtex(citation("apcluster"))
@

\bibliographystyle{plain}
\bibliography{apcluster}


\end{document}
