pedtools (version 0.9.0)

plotPedList: 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(plot.arg.list, widths = NA, frames = T,
  frametitles = NULL, fmar = NA, newdev = F, dev.height = NA,
  dev.width = NA, ...)

Arguments

plot.arg.list

A list of lists. Each element of plot.arg.list is a list, where the first element is the ped() object to be plotted, 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(plot.arg.list) if necessary, before passed on to layout(). Note that the vector does not need to sum to 1.

frames

Either a single logical (FALSE = no frames; TRUE = automatic framing) or a list of numeric vectors: Each vector must consist of consecutive integers, indicating subplots to be framed together. By default the framing follows the list structure of plot.arg.list.

frametitles

A character vector of titles for each frame. If this is non-NULL, titles for individuals subplots are ignored.

fmar

A single number in the interval \([0,0.5)\) controlling the position of the frames.

newdev

A logical, indicating if a new plot window should be opened.

dev.height, dev.width

The dimensions of the new device (only relevant if newdev is TRUE). If these are NA suitable values are guessed from the pedigree sizes.

…

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.

See Also

plot.ped()

Examples

# NOT RUN {
# Simplest use: Just give a list of ped objects.
# To guess suitable plot window dimensions, use 'newdev = TRUE'
peds = list(nuclearPed(3), cousinPed(2), singleton(12), halfSibPed())
plotPedList(peds, newdev = TRUE)

# Modify the relative widths (which are not guessed)
widths = c(2, 3, 1, 2)
plotPedList(peds, widths = widths)

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

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

# Non-default frames
frames = list(1, 2:3)
plotPedList(peds, widths = widths, frames = frames,
            frametitles = c('First', 'Second'))

# To give *the same* parameter to all plots, it can just be added at the end:
margins = c(2, 4, 2, 4)
title = 'Same title'
id.labels = ''
symbolsize = 1.5
plotPedList(peds, widths = widths, frames = frames, margins = margins,
            title = title, id.labels = id.labels, symbolsize = symbolsize,
            newdev = TRUE)

# COMPLEX EXAMPLE WITH MARKER DATA AND VARIOUS OPTIONS
# For more control of individual plots, each plot and all its parameters
# can be specified in its own list:
x1 = nuclearPed(nch = 3)
m1 = marker(x1, `3` = 1:2)
marg1 = c(7, 4, 7, 4)
plot1 = list(x1, marker = m1, margins = marg1, title = "Plot 1",
             deceased = 1:2, cex = 1.3)

x2 = cousinPed(2)
m2 = marker(x2, alleles = "A")
genotype(m2, leaves(x2)) = "A"
marg2 = c(3, 4, 2, 4)
plot2 = list(x2, marker = m2, margins = marg2, title = "Plot 2", symbolsize = 1.2,
             skip.empty.genotypes = TRUE, id = NULL)

x3 = singleton("Mr. X")
marg3 = c(10, 0, 0, 0)
plot3 = list(x3, margins = marg3, title = "Plot 3", symbolsize = 1, cex = 2)

x4 = halfSibPed()
shaded = 4:5
col = c("black", "black", "black", "blue", "blue")
marg4 = marg1
plot4 = list(x4, margins = marg4, title = "Plot 4", shaded = shaded, col = col)

plotPedList(list(plot1, plot2, plot3, plot4), widths = c(2,3,1,2),
            frames = list(1, 2:3, 4), newdev = TRUE)

# Different example:
plotPedList(list(halfCousinPed(4), cousinPed(7)),
            title = c('Many generations', 'Very many generations'),
            newdev = TRUE, dev.height = 9, dev.width = 9)


# }