R: Add points to the IBD triangle

showInTriangle {ribd}

R Documentation

Add points to the IBD triangle

Description

Utility function for plotting kappa coefficients in the IBD triangle. This was previously only implemented as a base R plot, but is now also available in ggplot2 and plotly formats, controlled by the argument plotType. Labels are often easier to read in the two latter versions: The ggplot2 version uses ggrepel to separate labels, while plotly enables interactive exploration of the plot.

Usage

showInTriangle(
  kappa,
  plotType = c("base", "ggplot2", "plotly"),
  new = TRUE,
  ped = NULL,
  pedBL = c(0.5, 0.5),
  pedArgs = NULL,
  col = 6,
  cex = 1,
  pch = 4,
  lwd = 2,
  jitter = NULL,
  labels = NULL,
  colLab = col,
  cexLab = 0.8,
  labSep = "-",
  pos = 1,
  adj = NULL,
  keep.par = TRUE,
  ...
)

Arguments

`kappa`	Coordinates of points to be plotted in the IBD triangle. Valid input types are: A numerical vector of length 2 (kappa0, kappa2) or 3 (kappa0, kappa1, kappa2). In the latter case kappa1 is ignored. A matrix of data frame, whose column names must include either `k0` and `k2`, `kappa0` and `kappa2`, or `ibd0` and `ibd2`. A list (and not a data frame), in which case an attempt is made to bind the elements row-wise.
`plotType`	Either "base" (default), "ggplot2" or "plotly". Abbreviations are allowed.
`new`	A logical indicating if a new triangle should be drawn.
`ped`	A pedigree to be drawn in the upper right corner of the plot. Default: NULL. This only works when `plotType` is `base` or `ggplot2`.
`pedBL`	A vector of length two, with entries in `⁠[0,1]⁠`, indicating the coordinates of the bottom left corner. Default: `c(0.5, 0.5)`.
`pedArgs`	Plotting arguments for the inset pedigree. Default: NULL.
`col`, `cex`, `pch`, `lwd`	Parameters controlling the appearance of points.
`jitter`	A logical. If NULL (default), jittering is disabled for `plotType`'s "base" or "ggplot2" and enabled for "plotly".
`labels`	A character of same length as the number of points, or a single logical `TRUE` or `FALSE`. If `TRUE`, labels are created by pasting columns `id1` and `id2` in `kappa` (if these exist) separated by `labSep`. By default, labels are disabled when `plotType = "base"`, enabled if `plotType = "ggplot2"` and enabled (interactively) if `plotType = "plotly"`.
`colLab`, `cexLab`, `pos`, `adj`	Parameters controlling the appearance of labels. Ignored when `plotType = "plotly"`.
`labSep`	A string, by default "-".
`keep.par`	A logical. If TRUE (and `plotType = "base"`), the graphical parameters are not reset after plotting, which may be useful for adding additional annotation.
`...`	Plot arguments passed on to `ibdTriangle()`.

Value

If plotType = 'base', the function returns NULL; otherwise the plot object.

Examples

showInTriangle(c(3/8, 1/8), label = "3/4 siblings", pos = 1)

# With inset pedigree
x = doubleCousins(1, 0, half2 = TRUE)
showInTriangle(c(3/8, 1/8), label = "3/4 siblings", pos = 1,
               ped = x, pedArgs = list(hatched = 6:7))

# All pairs
k = kappaIBD(x)
showInTriangle(k, labels = TRUE, pos = 1:4, ped = x)

# With jitter and variable colors
showInTriangle(k, labels = TRUE, pos = 1:4, jitter = TRUE, col = 1:7, ped = x)

# Separate labels (requires ggplot2 + ggrepel)
# showInTriangle(k, plot = "ggplot2", col = 2:8, ped = x)

# Interactive plot (requires plotly)
# showInTriangle(k, plot = "plotly", col = 2:8, pch = 0)