plotPedList: Plot a collection of pedigrees.
In pedtools: Creating and Working with Pedigrees and Marker Data

plotPedList

R Documentation

Plot a collection of pedigrees.

Description

This function creates a row of pedigree plots, each created by plot.ped(). Any parameter accepted by plot.ped() can be applied, either to all plots simultaneously, or to individual plots. Some effort is made to guess a reasonable window size and margins, but in general the user must be prepared to do manual resizing of the plot window. See various examples in the Examples section below.

Usage

plotPedList(
  plots,
  widths = NULL,
  groups = NULL,
  titles = NULL,
  frames = TRUE,
  fmar = NULL,
  source = NULL,
  dev.height = NULL,
  dev.width = NULL,
  newdev = !is.null(dev.height) || !is.null(dev.width),
  verbose = FALSE,
  ...
)

Arguments

`plots`	A list of lists. Each element of `plots` is a list, where the first element is a pedigree, and the remaining elements are passed on to `plot.ped`. These elements must be correctly named. See examples below.
`widths`	A numeric vector of relative widths of the subplots. Recycled to `length(plots)` if necessary, before passed on to `layout()`. Note that the vector does not need to sum to 1.
`groups`	A list of vectors, each consisting of consecutive integers, indicating subplots to be grouped. By default the grouping follows the list structure of `plots`.
`titles`	A character vector of titles for each group. Overrides titles given in individuals subplots.
`frames`	A logical indicating if groups should be framed.
`fmar`	A single number in the interval `[0,0.5)` controlling the position of the frames.
`source`	NULL (default), or the name or index of an element of `plots`. If given, marker data is temporarily transferred from this to all the other pedigrees. This may save some typing when plotting the same genotypes on several pedigrees.
`dev.height, dev.width`	The dimensions of the new plot window. If these are NA suitable values are guessed from the pedigree sizes.
`newdev`	A logical, indicating if a new plot window should be opened.
`verbose`	A logical.
`...`	Further arguments passed on to each call to `plot.ped()`.

Details

Note that for tweaking dev.height and dev.width the function dev.size() is useful to determine the size of the active device.

Author(s)

Magnus Dehli Vigeland

Examples

##################
# Basic examples #
##################

# Simples use: Just give a list of ped objects.
peds = list(nuclearPed(3), cousinPed(2), singleton(12), halfSibPed())
plotPedList(peds, newdev = TRUE)

# Override automatic determination of relative widths
w = c(2, 3, 1, 2)
plotPedList(peds, widths = w)

# In most cases the guessed dimensions are ok but not perfect.
# Resize plot window manually and re-plot with `newdev = FALSE` (default)
# plotPedList(peds, widths = w)

## Remove frames
plotPedList(peds, widths = w, frames = FALSE)

# Non-default grouping
plotPedList(peds, widths = w, groups = list(1, 2:3, 4), titles = 1:3)

# Parameters added in the main call are used in each sub-plot
plotPedList(peds, widths = w, labs = leaves, hatched = leaves,
            col = list(blue = males, red = females), symbolsize = 1.3)

dev.off()

#################################
# Example of automatic grouping #
#################################
H1 = nuclearPed()
H2 = singletons(id = c(1,3))

plotPedList(list(H1, H2), dev.height = 3, dev.width = 4,
            titles = c(expression(H[1]), expression(H[2])),
            cex = 1.5, cex.main = 1.3)

dev.off()

############################################################
# Complex example with individual parameters for each plot #
############################################################

# For more control of individual plots, each plot and all
# its parameters can be specified in its own list.

x1 = nuclearPed(nch = 3) |>
  addMarker(`3` = "1/2")
plot1 = list(x1, title = "Plot 1", marker = 1, deceased = 1:2, cex = 1.3,
             margins = c(7, 4, 7, 4))

x2 = cousinPed(2) |>
  addMarker(`11` = "A/A", `12` = "A/A")
plot2 = list(x2, title = "Family", marker = 1, symbolsize = 1.2, labs = NULL,
             margins = c(3, 4, 2, 4))

x3 = singleton("NN")
plot3 = list(x3, cex = 2, carrier = "NN", lty = c(NN = 2))

x4 = halfSibPed()
plot4 = list(x4, title = "Half sibs", cex = 1.3, hatched = leaves,
             col = list(red = founders), fill = list(blue = leaves),
             margins = c(7, 4, 7, 4))

plotPedList(list(plot1, plot2, plot3, plot4), widths = c(2,3,1,2),
            fmar = 0.03, groups = list(1, 2:3, 4), newdev = TRUE,
            cex.main = 1.5)

dev.off()

################################
# Example with large pedigrees #
################################

# Important to set device dimensions here

plotPedList(list(halfCousinPed(4), cousinPed(7)),
            titles = c("Large", "Very large"), widths = c(1, 1.3),
            dev.height = 8, dev.width = 6, margins = 1.5)

dev.off()

pedtools documentation built on Nov. 5, 2023, 5:06 p.m.