ribd: ibdDraw – R documentation

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ibdDraw

Colourised IBD plot

Description

This is a pedagogical tools for illustrating the concept of identity-by-descent, by representing the alleles in a pedigree by coloured points or letters. By default, the alleles are placed below each pedigree symbols, but any positions are possible, including inside. (See examples.)

Usage

ibdDraw(
  x,
  alleles,
  symbol = c("point", "text"),
  pos = 1,
  cols = NULL,
  cex = NA,
  sep = NULL,
  dist = 1,
  labs = FALSE,
  checkFounders = TRUE,
  checkParents = TRUE,
  margin = c(1, 1, 1, 1),
  ...
)

Arguments

`x`	A `ped` object.
`alleles`	A list of length `pedsize(x)`. Each element should consist of one or two integers, representing different colours. Zeroes produce "greyed-out" alleles.
`symbol`	Either "point" or "text".
`pos`	A vector recycled to the length of `labels(x)`, indicating allele placement relative to the pedigree symbols: 0 = inside; 1 = below; 2 = left; 3 = above; 4 = right. By default, all are placed below.
`cols`	A colour vector corresponding to the integers occurring in `alleles`.
`cex`	An expansion factor for the allele points/letters. Default: 3 for points and 2 for text.
`sep`	The separation between haplotypes within a pair, given as a multiple of the width of a pedigree symbol. Default: 0.5 when `pos = 0` and 1 otherwise.
`dist`	The distance between pedigree symbols and the alleles, given as a multiple of the height of a pedigree symbol. Default: 1. Ignored when `pos = 0`.
`labs`	A logical indicating if labels should be included.
`checkFounders`	A logical. If TRUE (default), a warning is issued if a founder has two equal alleles other than 0.
`checkParents`	A logical. If TRUE (default), a warning is issued if someone's alleles don't match those of the parents. This a superficial test and does not catch all Mendelian errors.
`margin`	Plot margins (bottom, left, top, right).
`...`	Further arguments passed on to `plot.ped()`.

Value

The plot structure is returned invisibly.

Examples

op = par(no.readonly = TRUE)

###############################
# Example 1: A family quartet #
###############################

x = nuclearPed(2)
als = list(1:2, 3:4, c(1,3), c(2,3))

# Default options
ibdDraw(x, als)

# Nicer colors
cols = c(7, 3, 2, 4)
ibdDraw(x, als, cols = cols)

# Inside the pedigree symbols
ibdDraw(x, als, cols = cols, pos = 0, symbolsize = 2.5)

# Other placements (margins depend on device - may need adjustment)
ibdDraw(x, als, cols = cols, pos = c(2, 4, 1, 1),
        margin = c(2, 6, 2, 6))

# Letters instead of points
ibdDraw(x, als, cols = cols, symbol = "text", cex = 2)

# Further arguments (note that `col` is an argument of `ped.plot()`)
ibdDraw(x, als, cols = cols, pos = 0, symbolsize = 2,
        labs = TRUE, shaded = 3:4, col = "blue")

# Mutations are warned about (unless `checkParents = FALSE`)
ibdDraw(x, alleles = list(1:2, 3:4, 5, 6))


############################
# Example 2: X inheritance #
############################

x = nuclearPed(2, sex = c(1, 2))
als = list(1, 2:3, 3, c(1, 3))
ibdDraw(x, als, cols = c(3, 7, 2))

#################################
# Example 3: mtDNA inheritance  #
#################################

x = linearPed(2, sex = 2)
als = list(1, 2, 2, 3, 2)
ibdDraw(x, als, cols = 2:4)


# Restore graphics parameters
par(op)

ribd

Pedigree-based Relatedness Coefficients

v1.2.0

GPL-3

Authors

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

Initial release