19.2 Biclustering

library(biclust)
tds <- matrix(rbinom(400, 50, 0.4), 20, 20)
res <- biclust(tds, method=BCCC(), delta=1.5, alpha=1, number=10)
res

## 
## An object of class Biclust 
## 
## call:
##  biclust(x = tds, method = BCCC(), delta = 1.5, alpha = 1, number = 10)
## 
## Number of Clusters found:  4 
## 
## First  4  Cluster sizes:
##                    BC 1 BC 2 BC 3 BC 4
## Number of Rows:       6    4    6    3
## Number of Columns:    5    6    4    6

bicluster(tds, res)

## $Bicluster1
##      [,1] [,2] [,3] [,4] [,5]
## [1,]   20   22   19   21   24
## [2,]   16   20   17   20   22
## [3,]   16   20   17   17   17
## [4,]   19   22   19   22   20
## [5,]   19   23   21   20   20
## [6,]   20   23   24   22   24
## 
## $Bicluster2
##      [,1] [,2] [,3] [,4] [,5] [,6]
## [1,]   19   19   18   23   19   19
## [2,]   22   22   18   24   24   19
## [3,]   21   19   19   20   22   21
## [4,]   18   21   17   19   19   18
## 
## $Bicluster3
##      [,1] [,2] [,3] [,4]
## [1,]   19   19   19   21
## [2,]   24   23   25   26
## [3,]   18   16   19   24
## [4,]   23   21   26   26
## [5,]   18   18   21   21
## [6,]   18   17   22   22
## 
## $Bicluster4
##      [,1] [,2] [,3] [,4] [,5] [,6]
## [1,]   21   18   15   24   15   19
## [2,]   23   21   14   24   15   19
## [3,]   24   19   18   22   18   19

parallelCoordinates(tds, res, number=4)

data(BicatYeast)
tds <- discretize(BicatYeast)
res <- biclust(tds, method=BCXmotifs(), alpha=0.05, number=50)
res

## 
## An object of class Biclust 
## 
## call:
##  biclust(x = tds, method = BCXmotifs(), alpha = 0.05, number = 50)
## 
## Number of Clusters found:  17 
## 
## First  5  Cluster sizes:
##                    BC 1 BC 2 BC 3 BC 4 BC 5
## Number of Rows:     172   99   45   34    9
## Number of Columns:    6    6    6    8   11

parallelCoordinates(BicatYeast, res, number=4)

plotclust(res, tds)

tds <- tribble(~x, ~y,
               1, 1,
               2, 1,
               1, 0,
               4, 7,
               3, 5,
               3, 6)

res <- biclust(as.matrix(tds), method=BCCC(), delta=50, alpha=0, number=5)
res

## 
## An object of class Biclust 
## 
## call:
##  biclust(x = as.matrix(tds), method = BCCC(), delta = 50, alpha = 0, 
##      number = 5)
## 
## There was one cluster found with
##   6 Rows and  2 columns

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