plot.ped: Plot pedigree

In pedtools: Creating and Working with Pedigrees and Marker Data

Plot pedigree

Description

This is the main function for plotting pedigrees. Many options are available for controlling the appearance of pedigree symbols and accompanying labels. The most important ones are illustrated in the Examples section below; for a complete overview, see the separate page internalplot, which also explains the plotting procedure in more detail.

Usage

## S3 method for class 'ped'
plot(x, draw = TRUE, keep.par = FALSE, ...)

drawPed(alignment, annotation = NULL, scaling = NULL, keep.par = FALSE, ...)

## S3 method for class 'pedList'
plot(x, ...)

## S3 method for class 'list'
plot(x, ...)

Arguments

x	A ped() object or a list of such.
draw	A logical, by default TRUE. If FALSE, no plot is produced, only the plotting parameters are returned.
keep.par	A logical, by default FALSE. If TRUE, the graphical parameters are not reset after plotting, which may be useful for adding additional annotation.
...	Arguments passed on to the internal plot functions. For a complete list of parameters, see internalplot. The most important ones are illustrated in the Examples below.
alignment	List of alignment details, as returned by .pedAlignment().
annotation	List of annotation details as returned by .pedAnnotation().
scaling	List of scaling parameters as returned by .pedScaling().

Details

The main pedigree layout is calculated with the kinship2 package, see kinship2::align.pedigree for details. Unlike kinship2, the implementation here also supports singletons, and plotting pedigrees as DAGs. In addition, some minor adjustments have been made to improve scaling and avoid unneeded duplications.

If x is a list of ped objects these are plotted next to each other, vertically centered in the plot window. For finer control, and possibly nested lists of pedigrees, use plotPedList().

Value

A list of three lists with various plot details: alignment, annotation, scaling.

See Also

plotPedList(), kinship2::plot.pedigree(). Plot options are documented in internalplot.

Examples

# Singleton
plot(singleton(1))

# Trio
x = nuclearPed(father = "fa", mother = "mo", child = "boy")
plot(x)

#' # Modify margins
plot(x, margins = 6)
plot(x, margins = c(0,0,6,6)) # b,l,t,r

# Larger text and symbols
plot(x, cex = 1.5)

# Enlarge symbols only
plot(x, symbolsize = 1.5)

# Various annotations
plot(x, hatched = "boy", starred = "fa", deceased = "mo", title = "Fam 1")

# Medical pedigree
plot(x, aff = "boy", carrier = "mo")

# Label only some members
plot(x, labs = c("fa", "mo"))

# Label males only
plot(x, labs = males)

# Rename some individuals
plot(x, labs = c(FATHER = "fa", "boy"))

# By default, labels are trimmed for initial/trailing line breaks ...
plot(x, labs = c("\nFA" = "fa"))

# ... but this can be overridden
plot(x, labs = c("\nFA" = "fa"), trimLabs = FALSE)

# Colours
plot(x, col = c(fa = "red"), fill = c(mo = "green", boy = "blue"))

# Non-black hatch colours are specified with the `fill` argument
plot(x, hatched = labels, fill = c(boy = "red"))

# Use functions to specify colours
plot(x, fill = list(red = leaves, blue = ancestors(x, "boy")))

# Line type and width
plot(x, lty = 2, lwd = 3, cex = 2)

# Detailed line type and width
plot(x, lty = list(dashed = founders), lwd = c(boy = 4))

# Include genotypes
x = addMarker(x, fa = "1/1", boy = "1/2", name = "SNP")
plot(x, marker = 1)

# Markers can also be called by name
plot(x, marker = "SNP")

# Plot as DAG (directed acyclic graph)
plot(x, arrows = TRUE, title = "DAG")

# Founder inbreeding is shown by default
founderInbreeding(x, "mo") = 0.1
plot(x)

# ... but can be suppressed
plot(x, fouInb = NULL)

# Other text above and inside symbols
plot(x, textAbove = letters[1:3], textInside = LETTERS[1:3])

# Plotting lists of pedigrees
plot(list(singleton(1), nuclearPed(1), linearPed(2)))

# Twins
x = nuclearPed(children = c("tw1", "tw2", "tw3"))
plot(x, twins = data.frame(id1 = "tw1", id2 = "tw2", code = 1)) # MZ
plot(x, twins = data.frame(id1 = "tw1", id2 = "tw2", code = 2)) # DZ

# Triplets
plot(x, twins = data.frame(id1 = c("tw1", "tw2"),
                           id2 = c("tw2", "tw3"),
                           code = 2))

# Selfing
plot(selfingPed(2))

# Complex pedigree: Quadruple half first cousins
plot(quadHalfFirstCousins())

# Straight legs
plot(quadHalfFirstCousins(), align = c(0,0))

# Use of `drawPed()`
dat = plot(nuclearPed(), draw = FALSE)
drawPed(dat$alignment, dat$annotation, dat$scaling)

pedtools documentation built on Nov. 5, 2023, 5:06 p.m.