pedtools: plot.ped – R documentation

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plot.ped

Plot pedigrees with genotypes

Description

This is the main function for pedigree plotting, with many options for controlling the appearance of pedigree symbols and accompanying labels. Most of the work is done by the plotting functionality in the kinship2 package.

Usage

## S3 method for class 'ped'
plot(
  x,
  marker = NULL,
  sep = "/",
  missing = "-",
  showEmpty = FALSE,
  labs = labels(x),
  title = NULL,
  col = 1,
  aff = NULL,
  carrier = NULL,
  hatched = NULL,
  shaded = NULL,
  deceased = NULL,
  starred = NULL,
  textInside = NULL,
  textAbove = NULL,
  hints = NULL,
  fouInb = "autosomal",
  margins = c(0.6, 1, 4.1, 1),
  keep.par = FALSE,
  ...
)

## S3 method for class 'singleton'
plot(
  x,
  marker = NULL,
  sep = "/",
  missing = "-",
  showEmpty = FALSE,
  labs = labels(x),
  title = NULL,
  col = 1,
  aff = NULL,
  carrier = NULL,
  hatched = NULL,
  shaded = NULL,
  deceased = NULL,
  starred = NULL,
  textInside = NULL,
  textAbove = NULL,
  fouInb = "autosomal",
  margins = c(8, 0, 0, 0),
  yadj = 0,
  ...
)

as_kinship2_pedigree(x, deceased = NULL, aff = NULL, hints = NULL)

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

Arguments

`x`	A `ped()` object.
`marker`	Either a vector of names or indices referring to markers attached to `x`, a `marker` object, or a list of such. The genotypes for the chosen markers are written below each individual in the pedigree, in the format determined by `sep` and `missing`. See also `showEmpty`. If NULL (the default), no genotypes are plotted.
`sep`	A character of length 1 separating alleles for diploid markers.
`missing`	The symbol (integer or character) for missing alleles.
`showEmpty`	A logical, indicating if empty genotypes should be included.
`labs`	A vector or function controlling the individual labels included in the plot. Alternative forms: If `labs` is a vector with nonempty intersection with `labels(x)`, these individuals will be labelled. If the vector is named, then the (non-empty) names are used instead of the ID label. (See Examples.) If `labs` is NULL, or has nonempty intersection with `labels(x)`, then no labels are drawn. If `labs` is the word "num", then all individuals are numerically labelled following the internal ordering. If `labs` is a function, it will be replaced with `labs(x)` and handled as above. (See Examples.)
`title`	The plot title. If NULL (default) or ”, no title is added to the plot.
`col`	A vector of colours for the pedigree members, recycled if necessary. Alternatively, `col` can be a list assigning colours to specific members. For example if `col = list(red = "a", blue = c("b", "c"))` then individual "a" will be red, "b" and "c" blue, and everyone else black. By default everyone is black.
`aff`	A vector of labels identifying members whose plot symbols should be filled. (This is typically used in medical pedigrees to indicate affected members.)
`carrier`	A vector of labels identifying members whose plot symbols should be marked with a dot. (This is typically used in medical pedigrees to indicate unaffected carriers of the disease allele.)
`hatched`	A vector of labels identifying members whose plot symbols should be hatched.
`shaded`	(Deprecated) synonym of `hatched`
`deceased`	A vector of labels indicating deceased pedigree members.
`starred`	A vector of labels indicating pedigree members that should be marked with a star in the pedigree plot.
`textInside, textAbove`	Character vectors of text to be printed inside or above pedigree symbols.
`hints`	A list with alignment hints passed on to `kinship2::align.pedigree()`. Rarely necessary, but see Examples.
`fouInb`	Either "autosomal" (default), "x" or NULL. If "autosomal" or "x", inbreeding coefficients are added to the plot above the inbred founders. If NULL, or if no founders are inbred, nothing is added.
`margins`	A numeric of length 4 indicating the plot margins. For singletons only the first element (the 'bottom' margin) is used.
`keep.par`	A logical (default = FALSE). If TRUE, the graphical parameters are not reset after plotting, which may be useful for adding additional annotation.
`...`	Arguments passed on to `plot.pedigree` in the `kinship2` package. In particular `symbolsize` and `cex` can be useful.
`yadj`	A tiny adjustment sometimes needed to fix the appearance of singletons.

Details

plot.ped is in essence an elaborate wrapper for kinship2::plot.pedigree().

Author(s)

Magnus Dehli Vigeland

Examples

x = nuclearPed(father = "fa", mother = "mo", child = "boy")
m = marker(x, fa = "1/1", boy = "1/2", name = "SNP")

plot(x, marker = m)

# Markers attached to `x` may be called by name
x = setMarkers(x, m)
plot(x, marker = "SNP")

# Other options
plot(x, marker = "SNP", hatched = typedMembers(x),
     starred = "fa", deceased = "mo")

# Filled symbols
plot(x, aff = males(x))

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

# Label only some members; rename the father
plot(x, labs = c(FATHER = "fa", "boy"))

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

# Colours
plot(x, col = list(red = "fa", green = "boy"), hatched = "boy")

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

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


#-----------------------------
# In some cases, the plotting machinery of `kinship2` needs a hint
# (see ?kinship2::align.pedigree)

# Example with 3/4-siblings
y = nuclearPed(2)
y = addChildren(y, 3, mother = 5, nch = 1)
y = addChildren(y, 4, mother = 5, nch = 1)

plot(y) # bad

hints = list(order = 1:7, spouse = rbind(c(3,5,0), c(5,4,0)))
plot(y, hints = hints) # good

pedtools

Creating and Working with Pedigrees and Marker Data

v0.9.7

GPL-3

Authors

Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)

Initial release