ribd (version 1.3.1)

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.

See Also

pedtools::plot.ped(), ibdsim2::haploDraw()

Examples

# NOT RUN {
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, hatched = 3:4, col = "blue")

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


##############################
# Example 2: Cousin pedigree #
##############################

x = swapSex(cousinPed(1), 3)
als = list(1:2, 3:4, NULL, c(1,3), c(2,3), NULL, 3, 3)

cols = c(7, 3, 2, 4)
ibdDraw(x, als, cols = cols, dist = 0.8)
ibdDraw(x, als, cols = cols, dist = 0.8, symbol = "text")

# Alternative: 0's give greyed-out alleles
als2 = list(1:2, 3:4, c(0,0), c(1,3), c(2,3), c(0,0), c(0,3), c(3,0))

ibdDraw(x, als2, cols = cols, dist = 0.8)
ibdDraw(x, als2, cols = cols, dist = 0.8, symbol = "text")


############################
# Example 3: 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 4: 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)

# }