plotPI: Creates Scatterplot Matrices for Probabilistic Indices.

Description Usage Arguments Details Author(s) References See Also Examples

Description

This function creates scatterplot matrices for the different probabilistic indices (PI) P_t , P_{tt'} and P_{tt't''} computed for different variables.

Usage

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  plotPI(X,g,type="pair",goi=NULL,mc=1,alg="Cnaive",col="black",
           highlight=NULL,hlCol="red",pch=20,zoom=FALSE,order=NULL,...)

Arguments

X

Matrix or vector with observations. Each column is a variable, each row an individual.

g

Vector of group labels for observations in X. Has to be the same length as X has observations.

type

Type of probabilistic index, see details.

goi

Groups of Interest, see details.

mc

Set the amount of cores to use for parallel calculation (only available for Linux).

order

Boolean, calculate PI only for natural order or for all combinations.

alg

Internal function, which implementation should be used to calculate the PI.

col

Vector of colors of the scatterplot.

highlight

Vector with positions, which are marked in special color.

hlCol

Color of highlighted spots.

pch

Dot type of the plot.

zoom

Logical, shall the plots be zoomed to interesting areas?

...

Additional plotting arguments.

Details

This function creates the scatterplot matrices for the PI, in case that they haven't been calculated previoulsy. This means that all arguments of the estPI are valid here, since this function is called first and the results will then be passed to the plot function of the estPI object.

See also plot.estPI for further details on the specific plot parameters.

Author(s)

Daniel Fischer

References

Fischer, D., Oja, H., Schleutker, J., Sen, P.K., Wahlfors, T. (2013): Generalized Mann-Whitney Type Tests for Microarray Experiments, Scandinavian Journal of Statistic, to appear.

Fischer, D., Oja, H. (2013): Mann-Whitney Type Tests for Microarray Experiments: The R Package gMWT, submitted article.

See Also

estPI, plot.estPI

Examples

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X <- c(sample(15))
g <- c(1,1,1,2,2,2,2,3,3,3,4,4,4,4,4)
estPI(X,g,type="single")

X <- matrix(c(rnorm(5000,1.5,2),rnorm(6000,2,2),rnorm(4000,3.5,1)),byrow=TRUE, ncol=10)
colnames(X) <- letters[1:10]
g <- c(rep(1,500),rep(2,600),rep(3,400))

plotPI(X,g,type="single",mc=1)


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