ORdensity (version 1.0)

plot.ORdensity: Plot function implemented by ORdensity class

Description

Plots a representation of the potential genes based on OR, FP and dFP.

Usage

# S3 method for ORdensity
plot(x, numclusters = x@bestKclustering, ...)

Arguments

x

Object of class ORdensity.

numclusters

By default NULL, it inherits from the x. Optionally, an integer number indicating number of clusters the genes are partitioned.

...

Optional arguments inherited from the generic plot method.

Value

Displays a plot with a representation of the potential genes based on OR (vertical axis), FP (horizontal axis) and dFP (size of the symbol is inversely proportional to its value). Moreover, genes identified as DE by the relaxed selection are represented by the symbol \(\bigtriangleup\).

Examples

# NOT RUN {
# Read data from 2 experimental conditions
simexpr_reduced <- simexpr[c(1:15,101:235),]
x <- simexpr_reduced[, 3:32]
y <- simexpr_reduced[, 33:62]
EXC.1 <- as.matrix(x)
EXC.2 <- as.matrix(y)
myORdensity <- new("ORdensity", Exp_cond_1 = EXC.1, Exp_cond_2 = EXC.2, B = 20)
plot(myORdensity)
# }