IBDtriangle | R Documentation |

The IBD triangle is typically used to visualize the pairwise relatedness of non-inbred individuals. Various annotations are available, including points marking the most common relationships, contour lines for the kinship coefficients, and shading of the unattainable region.

```
IBDtriangle(
relationships = c("UN", "PO", "MZ", "S", "H,U,G", "FC"),
kinshipLines = numeric(),
shading = "lightgray",
pch = 16,
cex_points = 1.2,
cex_text = 1.2,
axes = FALSE,
xlim = c(0, 1),
ylim = c(0, 1),
xlab = expression(kappa[0]),
ylab = expression(kappa[2]),
cex_lab = cex_text,
mar = c(3.1, 3.1, 1, 1),
xpd = TRUE,
keep.par = TRUE
)
```

`relationships` |
A character vector indicating relationships points to be included in the plot. See Details for a list of valid entries. |

`kinshipLines` |
A numeric vector (see Details). |

`shading` |
The shading colour for the unattainable region. |

`pch` |
Symbol used for the relationship points (see |

`cex_points` |
A number controlling the symbol size for the relationship points. |

`cex_text` |
A number controlling the font size for the relationship labels. |

`axes` |
A logical: Draw surrounding axis box? |

`xlim, ylim, mar, xpd` |
Graphical parameters; see |

`xlab, ylab` |
Axis labels |

`cex_lab` |
A number controlling the font size for the axis labels. |

`keep.par` |
A logical. If TRUE, the graphical parameters are not reset after plotting, which may be useful for adding additional annotation. |

For any pair of non-inbred individuals A and B, their genetic relationship
can be summarized by the IBD coefficients ```
(\kappa_0, \kappa_1,
\kappa_2)
```

, where `\kappa_i`

= P(A and B
share i alleles IBD at random autosomal locus). Since ```
\kappa_0 +
\kappa_1 + \kappa_2 = 1
```

, any relationship
corresponds to a point in the triangle in the ```
(\kappa_0,
\kappa_2)
```

-plane defined by ```
\kappa_0 \ge 0, \kappa_2
\ge 0, \kappa_0 + \kappa_2 \le 1
```

. The choice of `\kappa_0`

and
`\kappa_2`

as the axis variables is done for reasons of symmetry
and is not significant (other authors have used different views of the
triangle).

As shown by Thompson (1976), points in the subset of the triangle defined by
`4\kappa_0\kappa_2 > \kappa_1^2`

are
unattainable for pairwise relationships. By default this region is shaded in
light grey colour, but this can be modified with the `shading`

argument.

The IBD coefficients are linearly related to the kinship coefficient
`\phi`

by the formula

`\phi = 0.25\kappa_1 + 0.5\kappa_2.`

By indicating values for `\phi`

in the
`kinshipLines`

argument, the corresponding contour lines are shown as dashed
lines in the triangle plot.

The following abbreviations are valid entries in the `relationships`

argument:

UN = unrelated

PO = parent/offspring

MZ = monozygotic twins

S = full siblings

H,U,G = half sibling/avuncular (

**u**ncle)/grandparentFC = first cousins

SC = second cousins

DFC = double first cousins

Q = quadruple first half cousins

None

Magnus Dehli Vigeland

E. A. Thompson (1975).

*The estimation of pairwise relationships.*Annals of Human Genetics 39.E. A. Thompson (1976).

*A restriction on the space of genetic relationships.*Annals of Human Genetics 40.

`ibdEstimate()`

```
opar = par(no.readonly = TRUE) # store graphical parameters
IBDtriangle()
IBDtriangle(kinshipLines = c(0.25, 0.125), shading = NULL, cex_text = 0.8)
par(opar) # reset graphical parameters
```

forrel documentation built on Nov. 19, 2023, 5:14 p.m.

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