plotPedigree: Plot pedigree

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Plot pedigree

Description

Plot a pedigree using the "igraph" package. This function was inspired by plot.pedigree() from the "synbreed" package (under GPL-3). It add options for monoecious species and auto-fecondation.

Usage

plotPedigree(
  inds,
  mothers,
  fathers,
  generations,
  sexes = NULL,
  plot.it = TRUE,
  verbose = 1,
  edge.col.mother = "black",
  edge.col.father = "darkgrey",
  vertex.label.color = "darkblue",
  vertex.color = "white",
  vertex.size = 20,
  vertex.shape = "none",
  vertex.label.family = "Helvetica",
  mult.edge.curve = 0.25,
  edge.arrow.width = 0.75,
  edge.arrow.size = 0.75,
  xmin = -1,
  xmax = 1,
  ymin = -1,
  ymax = 1,
  ...
)

Arguments

inds	identifiers of the genotypes
mothers	identifiers of their mother; can be NA (case of the founders and haplodiploidization)
fathers	identifiers of their father; can be NA (case of the founders and haplodiploidization)
generations	should start at 0
sexes	"F" for female (circle), "M" for male (square) and "H" for hermaphrodite (triangle); can also be NA (no shape)
plot.it	if TRUE, the pedigree will be plotted
verbose	verbosity level (0/1/2)
edge.col.mother	see ?igraph.plotting
edge.col.father	see ?igraph.plotting
vertex.label.color	see ?igraph.plotting
vertex.color	see ?igraph.plotting
vertex.size	see ?igraph.plotting
vertex.shape	see ?igraph.plotting
vertex.label.family	see ?igraph.plotting
mult.edge.curve	see ?igraph.plotting
edge.arrow.width	see ?igraph.plotting
edge.arrow.size	see ?igraph.plotting
xmin	see norm_coords in the "igraph" package
xmax	see norm_coords in the "igraph" package
ymin	see norm_coords in the "igraph" package
ymax	see norm_coords in the "igraph" package
...	other plotting options; see ?plot.igraph and ?igraph.plotting

Value

invisible list with objects required to plot the pedigree

Author(s)

Timothee Flutre

See Also

subsetPedigree

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.