plot.ped: Plot pedigree
In magnusdv/pedtools: Creating and Working with Pedigrees and Marker Data

plot.ped

R Documentation

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 centred 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.

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")

#----- ID labels -----

# 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, long names are folded to width ~12 characters
plot(x, labs = c("Very long father's name" = "fa"), margin = 2)

# Folding width may be adjusted ...
plot(x, labs = c("Very long father's name" = "fa"), foldLabs = 6)

# ... or switched off (requires larger margin!)
plot(x, labs = c("Very long father's name" = "fa"), foldLabs = FALSE)

# 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")))

#----- Symbol line types and widths -----

# Dotted, thick symbols
plot(x, lty = 3, lwd = 4, cex = 2)

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

#----- Genotypes -----

x = nuclearPed(father = "fa", mother = "mo", child = "boy") |>
  addMarker(fa = "1/1", boy = "1/2", name = "SNP") |>
  addMarker(boy = "a/b")

# Show genotypes for first marker
plot(x, marker = 1)

# Show empty genotypes for untyped individuas
plot(x, marker = 1, showEmpty = TRUE)

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

# Multiple markers
plot(x, marker = 1:2)

#----- Further text annotation -----

# Founder inbreeding is shown by default
xinb = x |> setFounderInbreeding("mo", value = 0.1)
plot(xinb)

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

# Text can be placed around and inside symbols
plot(x, textAnnot = list(topright = 1:3, inside = LETTERS[1:3]))

# Use lists to add further options; see `?text()`
plot(x, margin = 2, textAnnot = list(
  topright = list(1:3, cex = 0.8, col = 2, font = 2, offset = 0.1),
  left = list(c(boy = "comment"), cex = 2, col = 4, offset = 2, srt = 20)))

# Exhaustive list of annotation positions
plot(singleton(1), cex = 3, textAnnot = list(top="top", left="left",
  right="right", bottom="bottom", topleft="topleft", topright="topright",
  bottomleft="bottomleft", bottomright="bottomright", inside="inside"))

#----- Special pedigrees -----

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

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

# 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))

# Lists of multiple pedigree
plot(list(singleton(1), nuclearPed(1), linearPed(2)))

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

magnusdv/pedtools documentation built on April 9, 2024, 7:35 a.m.