Description Usage Arguments Details Value Slots Constructor Accessors Signatures Functions that return objects of this class Extension to store results of other methods Author(s) See Also Examples
Factorization
is a class to store results of matrix
factorization algorithms. It has been designed for biclustering but
can be used for "principal component analysis",
"singular value decomposition", "independent component analysis",
"factor analysis", and "nonnegative matrix factorization".
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19  ## S4 method for signature 'Factorization'
plot(x, Rm=NULL, Cm=NULL, dim = c(1, 2),
zoom = rep(1, 2), col.group = NULL,
colors = c("orange1", "red", rainbow(length(unique(col.group)),
start=2/6, end=4/6)),
col.areas = TRUE, col.symbols = c(1, rep(2, length(unique(col.group)))),
sampleNames = TRUE, rot = rep(1, length(dim)),
labels = NULL, label.tol = 0.1, lab.size = 0.725, col.size = 10,
row.size = 10, do.smoothScatter = FALSE,
do.plot = TRUE, ... )
## S4 method for signature 'Factorization'
show(object)
## S4 method for signature 'Factorization'
showSelected(object, which=c(1,2,3,4))
## S4 method for signature 'Factorization'
summary(object, ...)


PLOT: 
x 
object of the class 
Rm 
row weighting vector. If 
Cm 
column weighting vector. If 
dim 
optional principal factors that are plotted along the
horizontal and vertical axis. Defaults to 
zoom 
optional zoom factor for row and column items. Defaults to

col.group 
optional vector (character or numeric) indicating the different groupings of the columns. Defaults to 1. 
colors 
vector specifying the colors for the annotation of the plot;
the first two elements concern the rows; the third till the last element
concern the columns; the first element will be used to color the unlabeled
rows; the second element for the labeled rows and the remaining elements to
give different colors to different groups of columns. Defaults to

col.areas 
logical value indicating whether columns should be
plotted as squares with areas proportional to their marginal mean
and colors representing the different groups ( 
col.symbols 
vector of symbols when 
sampleNames 
either a logical vector of length one or a character vector
of length equal to the number of samples in the dataset. If a
logical is provided, sample names will be displayed on the plot
( 
rot 
rotation of plot. Defaults to 
labels 
character vector to be used for labeling points on the graph;
if 
label.tol 
numerical value specifying either the percentile
( 
lab.size 
size of identifying labels for row and columnitems
as 
col.size 
size of the column symbols in mm. Defaults to 
row.size 
size of the row symbols in mm. Defaults to 
do.smoothScatter 
use smoothScatter or not instead of plotting
individual points. Defaults to 
do.plot 
produce a plot or not. Defaults to 
... 
further arguments are passed on to 

SHOW: 
object 
An instance of 

SHOWSELECTED: 

see 
which 
used to provide a list of which plots should be generated: 1=the information content of biclusters, 2=the information content of samples, 3=the loadings per bicluster, 4=the factors per bicluster, default c(1,2,3,4). 

SUMMARY: 

see 

... further arguments. 
Produces a biplot of a matrix factorization result stored in an instance of the Factorization class.
The function plot
is based on
the function plot.mpm
in the R package mpm
(Version: 1.016, Date: 20090826, Title: Multivariate Projection
Methods, Maintainer: Tobias Verbeke <[email protected]>,
Author: Luc Wouters <[email protected]>).
Biclusters are found by sparse factor analysis where both the factors and the loadings are sparse.
Essentially the model is the sum of outer products of vectors:
X = ∑_{i=1}^{p} λ_i z_i^T + U
where the number of summands p is the number of biclusters. The matrix factorization is
X = L Z + U
Here λ_i are from R^n, z_i from R^l, L from R^{n \times p}, Z from R^{p \times l}, and X, U from R^{n \times l}.
For noise free projection like independent component analysis we set the noise term to zero: U=0.
The argument label.tol
can be used to select the
most informative rows, i.e. rows that are most distant from the
center of the plot
(smaller 1: percentage of rows, larger 1: number of rows).
Only these rowitems are then labeled and represented as circles with their areas proportional to the row weighting.
If the columnitems are grouped these groups can be visualized by
colors given by col.group
.
Statistics of a matrix factorization result stored in an instance of the Factorization class.
This function supplies statistics on a matrix factorization result
which is stored as an instance of
Factorizationclass
.
The following is plotted:
the information content of biclusters.
the information content of samples.
the loadings per bicluster.
the factors per bicluster.
Lists selected statistics of a matrix factorization result stored in an instance of the Factorization class.
This function supplies selected statistics on a matrix factorization result
which is stored as an instance of
Factorizationclass
.
The following is plotted depending on the display selection
variable which
:
the information content of biclusters.
the information content of samples.
the loadings per bicluster.
the factors per bicluster.
Summary of matrix factorization result stored in an instance of the Factorization class.
This function gives information on a matrix factorization result
which is stored as an instance of
Factorizationclass
.
The summary consists of following items:
the number or rows and columns of the original matrix.
the number of clusters for rows and columns is given.
for the row cluster the information content is given.
for each column its information is given.
for each column cluster a summary is given.
for each row cluster a summary is given.

FACTORIZATION: 

An instance of 

PLOT: 
Rows 
a list with the X and Y coordinates of the rows and
an indication 
Columns 
a list with the X and Y coordinates of the columns. 

SHOW: 

no value. 

SHOWSELECTED: 

no value. 

SUMMARY: 

no value. 
Objects of class Factorization
have the following slots:
parameters
:Saves parameters of the factorization method in a list: ("method","number of cycles","sparseness weight","sparseness prior for loadings","sparseness prior for factors","number biclusters","projection sparseness loadings", "projection sparseness factors","initialization range","are loadings rescaled after each iterations","normalization = scaling of rows","centering method of rows","parameter for method").
n
:number of rows, left dimension.
p1
:right dimension of left matrix.
p2
:left dimension of right matrix.
l
:number of columns, right dimension.
center
:vector of the centers.
scaleData
:vector of the scaling factors.
X
:centered and scaled data matrix n x l.
L
:left matrix n x p1.
Z
:right matrix p2 x l.
M
:middle matrix p1 x p2.
LZ
:matrix L x M x Z.
U
:noise matrix.
avini
:information of each bicluster, vector of length p2.
xavini
:information extracted from each sample, vector of length l.
ini
:information of each bicluster in each sample, matrix p2 x l.
Psi
:noise variance per row, vector of length n.
lapla
:prior information for each sample, vector of length l.
Constructor of class Factorization.
Factorization(parameters=list(),n=1,p1=1,p2=1,l=1,center=as.vector(1),scaleData=as.vector(1),X=as.matrix(1),L=as.matrix(1),Z=as.matrix(1),M=as.matrix(1),LZ=as.matrix(1),U=as.matrix(1),avini=as.vector(1),xavini=as.vector(1),ini=as.matrix(1),Psi=as.vector(1),lapla=as.matrix(1))
In the following x
denotes a Factorization object.
parameters(x)
, parameters(x) < value
:
Returns or sets parameters
, where the return value and
value
are both an instance of list
. Parameters of the factorization
method are stored in a list: ("method","number of cycles","sparseness
weight","sparseness prior for loadings","sparseness prior for
factors","number biclusters","projection sparseness loadings",
"projection sparseness factors","initialization range","are loadings
rescaled after each iterations","normalization = scaling of
rows","centering method of rows","parameter for method").
n(x)
, n(x) < value
:
Returns or sets n
, where the return value and
value
are both an instance of numeric
. Number of rows, left dimension.
p1(x)
, p1(x) < value
:
Returns or sets p1
, where the return value and
value
are both an instance of numeric
. Right dimension of left matrix
p2(x)
, p2(x) < value
:
Returns or sets p2
, where the return value and
value
are both an instance of numeric
.
Left dimension of right matrix.
l(x)
, l(x) < value
:
Returns or sets l
, where the return value and
value
are both an instance of numeric
.
Number of columns, right dimension.
center(x)
, center(x) < value
:
Returns or sets center
, where the return value and
value
are both an instance of numeric
.
Vector of the centers.
scaleData(x)
, scaleData(x) < value
:
Returns or sets scaleData
, where the return value and
value
are both an instance of numeric
.
Vector of the scaling factors.
X(x)
, X(x) < value
:
Returns or sets X
, where the return value and
value
are both an instance of matrix
.
Centered and scaled data matrix n x l.
L(x)
, L(x) < value
:
Returns or sets L
, where the return value and
value
are both an instance of matrix
.
Left matrix n x p1.
Z(x)
, Z(x) < value
:
Returns or sets Z
, where the return value and
value
are both an instance of matrix
.
Right matrix p2 x l.
M(x)
, M(x) < value
:
Returns or sets M
, where the return value and
value
are both an instance of matrix
.
Middle matrix p1 x p2.
LZ(x)
, LZ(x) < value
:
Returns or sets LZ
, where the return value and
value
are both an instance of matrix
.
Matrix L x M x Z.
U(x)
, U(x) < value
:
Returns or sets U
, where the return value and
value
are both an instance of matrix
.
Noise matrix.
avini(x)
, avini(x) < value
:
Returns or sets avini
, where the return value and
value
are both an instance of numeric
.
Information of each bicluster, vector
of length p2.
xavini(x)
, xavini(x) < value
:
Returns or sets xavini
, where the return value and
value
are both an instance of numeric
.
Information extracted from each sample, vector
of length l.
ini(x)
, ini(x) < value
:
Returns or sets ini
, where the return value and
value
are both an instance of matrix
.
Information of each bicluster in each
sample, matrix p2 x l.
Psi(x)
, Psi(x) < value
:
Returns or sets Psi
, where the return value and
value
are both an instance of numeric
.
Noise variance per row, vector of length n.
lapla(x)
, lapla(x) < value
:
Returns or sets lapla
, where the return value and
value
are both an instance of matrix
.
Prior information for each sample,
vector of length l.
signature(x = "Factorization", y = "missing")
Plot of a matrix factorization result
signature(object = "Factorization")
Display statistics of a matrix factorization result
signature(object = "Factorization", which =
"numeric")
Display particular statistics of a matrix factorization result
signature(object = "Factorization")
Summary of matrix factorization result
Factorization objects are returned by fabia
, fabias
, fabiap
,
fabiasp
, mfsc
, nmfsc
,
nmfdiv
, and nmfeu
.
The class Factorization
may contain the result of different matrix factorization
methods. The methods may be generative or not.
Methods my be "singular value decomposition" (M contains singular values as well as avini, L and Z are orthonormal matrices), "independent component analysis" (Z contains the projection/sources, L is the mixing matrix, M is unity), "factor analysis" (Z contains factors, L the loadings, M is unity, U the noise, Psi the noise covariance, lapla is a variational parameter for nonGaussian factors, avini and ini are the information the factors convey about the observations).
Sepp Hochreiter
fabia
,
fabias
,
fabiap
,
fabi
,
fabiasp
,
mfsc
,
nmfdiv
,
nmfeu
,
nmfsc
,
extractPlot
,
extractBic
,
plotBicluster
,
Factorization
,
projFuncPos
,
projFunc
,
estimateMode
,
makeFabiaData
,
makeFabiaDataBlocks
,
makeFabiaDataPos
,
makeFabiaDataBlocksPos
,
matrixImagePlot
,
fabiaDemo
,
fabiaVersion
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106  ###################
# TEST
###################
#
# PLOT
#
n=200
l=100
p=4
dat < makeFabiaDataBlocks(n = n,l= l,p = p,f1 = 5,f2 = 5,
of1 = 5,of2 = 10,sd_noise = 3.0,sd_z_noise = 0.2,mean_z = 2.0,
sd_z = 1.0,sd_l_noise = 0.2,mean_l = 3.0,sd_l = 1.0)
X < dat[[1]]
ZC < dat[[3]]
LC < dat[[4]]
resEx < fabia(X,p,0.01,400)
gclab < rep.int(0,l)
gllab < rep.int(0,n)
clab < as.character(1:l)
llab < as.character(1:n)
for (i in 1:p){
for (j in ZC[i]){
clab[j] < paste(as.character(i),"_",clab[j],sep="")
}
for (j in LC[i]){
llab[j] < paste(as.character(i),"_",llab[j],sep="")
}
gclab[unlist(ZC[i])] < gclab[unlist(ZC[i])] + p^i
gllab[unlist(LC[i])] < gllab[unlist(LC[i])] + p^i
}
groups < gclab
colnames(X(resEx)) < clab
rownames(X(resEx)) < llab
plot(resEx,dim=c(1,2),label.tol=0.1,col.group = groups,lab.size=0.6)
plot(resEx,dim=c(1,3),label.tol=0.1,col.group = groups,lab.size=0.6)
plot(resEx,dim=c(2,3),label.tol=0.1,col.group = groups,lab.size=0.6)
#
# SHOW
#
dat < makeFabiaDataBlocks(n = 100,l= 50,p = 3,f1 = 5,f2 = 5,
of1 = 5,of2 = 10,sd_noise = 3.0,sd_z_noise = 0.2,mean_z = 2.0,
sd_z = 1.0,sd_l_noise = 0.2,mean_l = 3.0,sd_l = 1.0)
X < dat[[1]]
resEx < fabia(X,3,0.01,100)
show(resEx)
#
# SHOWSELECTED
#
dat < makeFabiaDataBlocks(n = 100,l= 50,p = 3,f1 = 5,f2 = 5,
of1 = 5,of2 = 10,sd_noise = 3.0,sd_z_noise = 0.2,mean_z = 2.0,
sd_z = 1.0,sd_l_noise = 0.2,mean_l = 3.0,sd_l = 1.0)
X < dat[[1]]
resEx < fabia(X,3,0.01,100)
showSelected(resEx,which=1)
showSelected(resEx,which=2)
#
# SUMMARY
#
dat < makeFabiaDataBlocks(n = 100,l= 50,p = 3,f1 = 5,f2 = 5,
of1 = 5,of2 = 10,sd_noise = 3.0,sd_z_noise = 0.2,mean_z = 2.0,
sd_z = 1.0,sd_l_noise = 0.2,mean_l = 3.0,sd_l = 1.0)
X < dat[[1]]
resEx < fabia(X,3,0.01,100)
summary(resEx)

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