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Last data update: 2014.03.03

R: Visualize results of 'link{findThreshold}'

plotDistances

R Documentation

Visualize results of `link{findThreshold}`

Description

The functions plotDistances and plotMutinfo are used to visualize the distance threshold calculated by findThreshold in the context of pairwise distances among objects in the reference set.

Usage

plotDistances(distances, D = NA, interval = NA,
              ylab = "distances", ...)

plotMutinfo(breaks, D = NA, interval = NA,
            xlab = "distance", ylab = "mutual information", ...)

Arguments

`distances`	The `$distances` element of the output value of `findThreshold`
`breaks`	The `$breaks` element of the output value of `findThreshold`
`D`	The distance threshold
`interval`	The range of values over which candidiate values of PMMI are evaluated.
`xlab`	Label the x axis of the plot.
`ylab`	Label the y axis of the plot.
`...`	Additional arguments are passed to `bwplot` (`plotDistances`) or `xyplot`

(plotMutinfo)

Details

plotDistances produces a box-and-whisker plot contrasting within- and between-group distances. plotMutinfo produces a plot of cutpoints vs mutual information scores.

Value

Returns a lattice grid object.

Author(s)

Noah Hoffman

Examples

data(iris)
dmat <- as.matrix(dist(iris[,1:4], method="euclidean"))
groups <- iris$Species
thresh <- findThreshold(dmat, groups)
do.call(plotDistances, thresh)
do.call(plotMutinfo, thresh)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(clst)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/clst/plotDistances.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDistances
> ### Title: Visualize results of 'link{findThreshold}'
> ### Aliases: plotDistances plotMutinfo
> ### Keywords: classif
> 
> ### ** Examples
> 
> data(iris)
> dmat <- as.matrix(dist(iris[,1:4], method="euclidean"))
> groups <- iris$Species
> thresh <- findThreshold(dmat, groups)
> do.call(plotDistances, thresh)
> do.call(plotMutinfo, thresh)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

Visualize results of link{findThreshold}