dvir (version 3.3.0)

plotDVI: Plot a DVI problem

Description

Plot a DVI problem

Usage

plotDVI(
  dvi,
  pm = TRUE,
  am = TRUE,
  style = 1,
  famnames = NA,
  hatched = typedMembers,
  frames = TRUE,
  titles = c("PM", "AM"),
  cex = NA,
  col = 1,
  lwd = 1,
  fill = NA,
  carrier = NULL,
  widths = NULL,
  heights = NULL,
  nrowPM = NA,
  nrowAM = NA,
  dev.height = NULL,
  dev.width = NULL,
  newdev = !is.null(c(dev.height, dev.width)),
  ...
)

Arguments

dvi

A dviData object, typically created with dviData().

pm

Either a logical indicating if the PM data should be plotted (as a set of singletons), or a vector of indices selecting a subset of the PM samples. Default: TRUE.

am

Either a logical indicating if the AM families data should be plotted, or a vector of indices selecting a subset of the families. Default: TRUE.

style

An integer (currently 1 or 2) indicating the style of the plot.

famnames

A logical. If NA (default) family names are included if there are multiple families.

hatched

A character vector of ID labels, or the name of a function. By default, typed individuals are hatched.

frames

A logical, by default TRUE.

titles

A character of length 2.

fill, cex, col, lwd, carrier

Arguments passed on to pedtools::plot.ped().

widths, heights

Numeric with relative columns widths / row heights, to be passed on to layout().

nrowPM

The number of rows in the array of PM singletons.

nrowAM

The number of rows in the array of AM families.

dev.height, dev.width

Plot height and widths in inches. These are optional, and only relevant if newdev = TRUE.

newdev

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

...

Further parameters to be passed on to pedtools::plot.ped(), e.g., marker, cex, cex.main, symbolsize.

Examples

plotDVI(example2)

# Override default layout of PM singletons
plotDVI(example2, nrowPM = 1)

# Subset
plotDVI(example2, pm = 1:2, am = 1, titles = c("PM (1-2)", "AM (1)"))

# AM only
plotDVI(example2, pm = FALSE, titles = "AM families")

# Further plot options
plotDVI(example2, frames = FALSE, marker = 1, cex = 1.2, nrowPM = 3, nrowAM = 2,
  textAnnot = list(inside = list(c(M1 = "?", M2 = "?", M3 = "?"), cex = 1.5)))