R: Struct Plots of Observations Based on Posterior Probabilities

plotstruct {phyclust}

R Documentation

Struct Plots of Observations Based on Posterior Probabilities

Description

This function provides structure plots of data set given based on posterior probabilities, the Z.normalized matrix.

Usage

plotstruct(Z, X.class = NULL, sort.inside.class = TRUE,
    direction = "h", main = "Structure Plot", xlab = "Observations",
    ylab = "Posterior Probabilities", ...)

Arguments

`Z`	a Z matrix as Z.normalized in `Class phyclust`.
`X.class`	class ids indicated for all observations
`sort.inside.class`	sort observations inside class by max posteriors.
`direction`	either "h" for horizontal or "v" for vertical.
`main`	main label, default = "Structure Plot".
`xlab`	x-axis label, default = "Observations".
`ylab`	y-axis label, default = "Posterior Probabilities".
`...`	other options passed to `plot`.

Details

The posterior probabilities in ret.phyclust$Z.normalized will be drawn in colors.

If X.class is submitted, the plot will draw in the order of class ids and the sort.inside.class will be skipped.

Value

A structure plot will be drawn.

Author(s)

Wei-Chen Chen wccsnow@gmail.com

References

Phylogenetic Clustering Website: http://snoweye.github.io/phyclust/

Examples

## Not run: 
library(phyclust, quiet = TRUE)

set.seed(1234)
ret.1 <- phyclust(seq.data.toy$org, 3)
plotstruct(ret.1$Z.normalized)
windows()
plotstruct(ret.1$Z.normalized, sort.inside.class = FALSE)

# With class ids
X.class <- as.numeric(gsub(".*-(.*)", "\\1", seq.data.toy$seqname))
windows()
plotstruct(ret.1$Z.normalized, X.class = X.class)

## End(Not run)

[Package phyclust version 0.1-18 Index]