plot.IBD: Plot IBD patterns and pattern distributions

Description

Plot IBD patterns and pattern distributions

Usage

# S3 method for IBD
plot(x,labels=NULL,probs=NULL,order=NULL,colrs=c('black','red','blue'), 
digits=3,nr=ceiling(sqrt(np)),...)

Value

No value is returned, the function is called for its side effect, a plot on the current display device.

Arguments

x: A matrix whose rows are IBD patterns, or a list whose components are patt, such a matrix, together with pr, a vector of the corresponding probabilities
labels: Vector of numerical or character labels for the patterns, if NA, labels are constructed from the patterns by catenation, if NULL, the labels are not displayed.
probs: Vector of probabilities of the patterns, if not provided as a component of pattern; if NULL, the probabilities are not displayed.
order: A character string, partially matched using pmatch to one of 'pattern', 'probs', or 'labels', requesting ordering diagram accordingly (in the case of probs in decreasing order, or a numeric, complex, character or logical vector of length the number of patterns, requesting ordering by this variable, or NULL (the default), requesting no re-ordering.
colrs: A vector of colours: ties in the ordering variable are indicated by coloured groups, with colours chosen cyclically from this vector.
digits: Integer, overwriting default number of significant digits for probs
nr: Integer, overwriting default number of rows for plotted array, default a rounding up of the square root of the number of patterns.
...: additional arguments to plot

Author

Peter Green (P.J.Green@bristol.ac.uk)

Examples

Run this code

require(ribd)
data(emperors)

plot.IBD(convertIBD('3cousins-star'),order='probs',col=c('blue','red','black'))

plot(attr(emperors,'ped'))

o<-order(emperors$pr)[1:12]
plot.IBD(emperors$patt[o,],probs=emperors$pr[o],labels=NA,order='probs')

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