plot.simfam: Plot method for 'simfam' or Plot pedigrees

Description Usage Arguments Details Value See Also Examples

View source: R/plot.simfam.R

Description

Provides pedigree plots for specified families generated from simfam function with option to save plots into a pdf file or for dataframe containing required .

Usage

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## S3 method for class 'simfam'
plot(x, famid, pdf=FALSE, file=NULL, ...)

Arguments

x

An object of class 'simfam' created by simfam function or a data frame that has class attributes c("simfam", "data.frame").

famid

List of family IDs to plot. Default is the first family in given data set.

pdf

Logical; if TRUE, pedigree plots are saved in a pdf file. If FALSE, plot pedigrees on current plotting device. Default is FALSE.

file

File name to save the pedigree plots; Default file name is "pedigreeplot.pdf".

...

Additional arguments passed on to the plot function.

Details

Argument x can be a data frame that contains famID, indID, fatherID, motherID, gender (1 for male, 0 for female), status (1 for affected, 0 for non-affected), mgene (1 for mutation carrier, 0 for non-carrier, NA for missing), and proband (1 for proband, 0 for non-proband) and should have class attributes class(x) <- c("simfam", "data.frame").

Optionally, the data frame can contain a column named carrp.geno or carrp.pheno to replace missing values in mgene with their carrier probabilities.

Value

Returns pedigree plots for specified families created by simfam function or dataframe provided along with the affection and carrier mutation statuses of family members. Probands from each pedigree are indicated using red color.

When object inlcudes carrp.geno and/or carrp.pheno generated by carrierprob function, the plot function displays the carrier probabilities for those with missing carrier status.

See Also

simfam, summary.simfam, carrierprob

Examples

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# Simulated family data

fam <- simfam(N.fam=300, design="pop+", base.dist="Weibull", allelefreq=0.02, 
       base.parms=c(0.01,3), vbeta=c(-1.13, 2.35), agemin=20)
 
# Pedigree plots for first three simulated families

plot(fam, famid=c(1:3), pdf=TRUE, file="pedigrees.pdf")
	


FamEvent documentation built on May 20, 2017, 5:39 a.m.
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