## 19.2 Biclustering

THIS SECTION IS UNDER DEVELOPMENT. PLEASE CHECK BACK LATER

20200902

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:       7    6    4    3
## Number of Columns:    5    6    6    7
bicluster(tds, res)
## $Bicluster1 ## [,1] [,2] [,3] [,4] [,5] ## [1,] 22 21 22 19 18 ## [2,] 17 22 18 17 19 ## [3,] 23 25 24 20 20 ## [4,] 23 23 23 24 22 ## [5,] 18 18 19 16 17 ## [6,] 20 23 22 23 21 ## [7,] 25 24 21 21 20 ## ##$Bicluster2
##      [,1] [,2] [,3] [,4] [,5] [,6]
## [1,]   21   21   17   19   20   24
## [2,]   19   19   16   18   17   21
## [3,]   24   22   22   18   21   23
## [4,]   24   19   19   19   21   24
## [5,]   19   19   15   16   18   21
## [6,]   21   19   16   15   22   19
##
## $Bicluster3 ## [,1] [,2] [,3] [,4] [,5] [,6] ## [1,] 21 21 21 20 22 17 ## [2,] 21 22 22 20 22 20 ## [3,] 14 20 18 19 16 14 ## [4,] 15 17 15 17 17 16 ## ##$Bicluster4
##      [,1] [,2] [,3] [,4] [,5] [,6] [,7]
## [1,]   18   18   18   20   18   22   20
## [2,]   16   24   21   20   23   25   25
## [3,]   16   21   17   19   18   21   20
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:  15
##
## First  5  Cluster sizes:
##                    BC 1 BC 2 BC 3 BC 4 BC 5
## Number of Rows:     146  119   52   24   15
## Number of Columns:    6    7    6    8   10
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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