Description Usage Arguments Examples
cobra_pod
performs convex biclustering on incomplete data matrices using an MM algorithm.
1 2 | cobra_pod(X, Lambda_row, Lambda_col, E_row, E_col, w_row, w_col, Theta,
max_iter = 100, tol = 0.001, max_iter_inner = 1000, tol_inner = 1e-04)
|
X |
The data matrix to be clustered. The rows are the features, and the columns are the samples. |
Lambda_row |
Initial guess of row Langrage multipliers |
Lambda_col |
Initial guess of column Langrage multipliers |
E_row |
Edge-incidence matrix for row graph |
E_col |
Edge-incidence matrix for column graph |
w_row |
Vector of weights for row graph |
w_col |
Vector of weights for column graph |
Theta |
A vector of missing indices - row major order |
max_iter |
Maximum number of iterations |
tol |
Stopping criterion |
max_iter_inner |
Maximum number of inner cobra iterations |
tol_inner |
Stopping criterion for inner cobra loop |
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 | ## Create bicluster path
## Example: Lung
X <- lung
X <- X - mean(X)
X <- X/norm(X,'f')
## Create annotation for heatmap
types <- colnames(lung)
ty <- as.numeric(factor(types))
cols <- rainbow(4)
YlGnBu5 <- c('#ffffd9','#c7e9b4','#41b6c4','#225ea8','#081d58')
hmcols <- colorRampPalette(YlGnBu5)(256)
## Construct weights and edge-incidence matrices
phi <- 0.5; k <- 5
wts <- gkn_weights(X,phi=phi,k_row=k,k_col=k)
w_row <- wts$w_row
w_col <- wts$w_col
E_row <- wts$E_row
E_col <- wts$E_col
## Connected Components of Row and Column Graphs
wts$nRowComp
wts$nColComp
## Generate random initial dual variables
set.seed(12345)
n <- ncol(X); p <- nrow(X)
m_row <- nrow(E_row); m_col <- nrow(E_col)
Lambda_row <- matrix(rnorm(n*m_row),n,m_row)
Lambda_col <- matrix(rnorm(p*m_col),p,m_col)
#### Initialize path parameters and structures
gam <- 200
## Create random mask
nMissing <- floor(0.1*n*p)
Theta <- sample(1:(n*p), nMissing, replace=FALSE)
sol <- cobra_pod(X,Lambda_row,Lambda_col,E_row,E_col,gam*w_row,gam*w_col,Theta)
heatmap(sol$U,col=hmcols,labRow=NA,labCol=NA,ColSideCol=cols[ty])
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.