plot.biomarker: Plot function for '"biomarker"' objects

In walachja/Biomarker: Biomarker identification

Description

Plotting object of class "biomarker", which is result of function biomarker

Usage

plot.biomarker(x, type="Vstar",...)

Arguments

x	object of the type biomarker
type	possible type of the plot: "Vstar" and "diag". In first case the normalized values of V statistic (V*), otherwise cell outlier diagnostics is plotted.
...	another arguments, curently not being used.

Details

If type="Vstar", all the values above the treashold (dotted line) were identified as biomarkers. If type="diag", a graphical representation of outlyingness of each cell is plotted. Continuous gray scale is used, where black represents "biggest" outliers. Stars on the top of plot indicates the positions of the biomarkers.

Author(s)

Jan Walach

See Also

biomarker,

Examples

# Data simulation
set.seed(4523)
n <- 40; p <- 50
r <- runif(p, min = 1, max = 10)
conc <- runif(p, min = 0, max = 1)*5+matrix(1,p,1)*5
a <- conc*r
S <- rnorm(n,0,0.3)%*%t(rep(1,p))
B <- matrix(rnorm(n*p,0,0.8),n,p)
R <- rep(1,n)%*%t(r)
M <- matrix(rnorm(n*p,0,0.021),n,p)
# Fifth observation is outlier
M[5,] <- M[5,]*3 + sample(c(0.5,-0.5),replace=TRUE,p)
C <- rep(1,n)%*%t(conc)
C[1:20,c(2,15,28,40)] <- C[1:20,c(2,15,28,40)]+matrix(1,20,4)*1.8
X <- (1-S)*(C*R+B)*exp(M)

# Biomarker identification
b <- biomarker(X,g1=1:20,g2=21:40,type ="tau")

plot(b,type="diag")
plot(b,type="Vstar")

walachja/Biomarker documentation built on May 3, 2019, 5:21 p.m.