toscca (version 0.1.0)

plt.selstab: Plot slection stability for penalty parameter performance.

Description

This function plots cv for different thresholds

Usage

plt.selstab(
  object,
  X,
  Y,
  nonz_x,
  nonz_y,
  palette_values = mpalette,
  blue = TRUE,
  mm = TRUE,
  k = 1
)

Value

No return value, called for selection stability pot.

Arguments

object

A toscca object.

X

nxp matrix. Observation matrix.

Y

A nxq matrix. Observation matrix.

nonz_x

Numeric vector. Sparsity levels of X.

nonz_y

Numeric vector. Sparsity levels of Y.

palette_values

Character. Name of a palette for the heatmap. Default is "Teal".

blue

Logical. If TRUE, use only scale of blues from palette.

mm

Logic. Indicates whether there are multiple measurements or not. Default is True.

k

Numeric. Component, default k =1.

Examples

# \donttest{
# example code
#sample size etc
N = 10
p = 25
q = 5
# noise
X0 = sapply(1:p, function(x) rnorm(N))
Y0 = sapply(1:q, function(x) rnorm(N))

colnames(X0) = paste0("x", 1:p)
colnames(Y0) = paste0("y", 1:q)

# signal
Z1 = rnorm(N,0,10)


#Some associations with the true signal
alpha = (6:10) / 10
beta  = -(2:3) / 10

loc_alpha = 1:length(alpha)
loc_beta  = 1:length(beta)

for(j in 1:length(alpha))
  X0[, loc_alpha[j]] =  alpha[j] * Z1 + rnorm(N,0,0.03)

for(j in 1:length(beta))
  Y0[, loc_beta[j]] =  beta[j] * Z1 + rnorm(N,0,0.03)

# performa toscca
X = standardVar(X0)
Y = standardVar(Y0)
K = 2                                       # number of components to be estimated
nonz_x = c(2,5, 10, 20)                     # number of nonzero variables for X
nonz_y = c(2, 3, 4)                      # number of nonzero variables for Y
init   = "uniform"                          # type of initialisation
cca_toscca  = toscca(X, Y, nonz_x, nonz_y, K, alpha_init = init,
combination = TRUE, K=1, silent = TRUE, toPlot = FALSE)
plt <- plt.selstab(cca_toscca,X, Y, nonz_x = nonz_x, nonz_y = nonz_y, mm=FALSE)
# }