ggdraw.pedigree: Plot Pedigree Using ggplot2

In moritzlindner/ggped: Draws pedigrees using ggplot and kinship2

Plot Pedigree Using ggplot2

Description

This function generates a pedigree plot using ggplot2.

Usage

ggdraw.pedigree(
  dat = NULL,
  features = c("affected"),
  features.as.lables = NULL,
  plot.names = T,
  plot.kinship.label = T,
  column.names = list(x = "x", y = "y", Name = "Name", mate.id = "mate.id", twin.id =
    "twin.id", mate.centerpoint = "mate.centerpoint", family.centerpoint =
    "family.centerpoint", twin.centerpoint = "twin.centerpoint", sex = "sex", adopted =
    "adopted", pregnancy = "pregnancy"),
  col.palette = suppressWarnings(brewer.pal(length(unique(dat[, features.as.lables])),
    "Set2")),
  col.lables = c(`wt/wt` = "black", wt = "black", `+/+` = "black", `wt/mut` =
    col.palette[1], het = col.palette[1], `+/-` = col.palette[1], `mut/mut` =
    col.palette[2], hom = col.palette[2], `-/-` = col.palette[2]),
  col.tree = "#000000",
  col.double = "#808080",
  chrtype = "autosome",
  packed = TRUE,
  align = TRUE,
  width = 10,
  allow.repeated = F,
  ...
)

Arguments

dat	A pedigree object as returned by pedigree or data frame in the format as returned by dfalign.pedigree.
features	Names of columns containing binary features (e.g. affected status) in dat.
features.as.lables	Names of columns containing nominal features for plotting as labels under the subject's name.
plot.names	Whether to plot names of subjects or not. Requires a defined column in dat containing names.
plot.kinship.label	Whether to calculate and plot degree of kinship for inbred matings.
column.names	If dat is a data frame, then column name definitions. Standard are those created by dfalign.pedigree. adopted and pregancy are additional optional logical columns.
col.palette	Palette to use for text features.
col.lables	Font colour for subject labels. Per default, sets *wt* to black, *het* to first colour of palette and *hom* to the second colour of the palette. Accepts any arguments that is understood by the parameter *values* of scale_colour_manual.
col.tree	Line colour for tree.
col.double	Line colour for lines between repeatedly plotted subjects.
chrtype	chromosome type. The currently supported types are "autosome" and "X" or "x".
packed	should the pedigree be compressed, i.e., to allow diagonal lines connecting parents to children in order to have a smaller overall width for the plot.
align	for a packed pedigree, align children under parents (TRUE), to the extent possible given the page width, or align to to the left margin (FALSE). The latter is mostly used by internal routines.
width	for a packed output, the minimum width
allow.repeated	Allow drawing pedigress where subjects need to appear multiple times. This currently usually results in faulty pedigrees.
...	Further arguments passed to geom_pedigreepoint.

Value

A ggplot object containing the pedigree

Examples

data(minnbreast)
bpeds <- with(minnbreast,pedigree(id, fatherid, motherid, sex, affected=proband, famid=famid))
# pedigree with id=8
bped.id8 <- bpeds['8']
# convert into ggplot-compatible data frame
df<-dfalign.pedigree(bped.id8)
cartesian<-ggdraw.pedigree(dat=df,features = c("affected"))
cartesian+
 scale_x_continuous(expand=expansion(add = 0.25))+
  scale_y_reverse(expand=expansion(add = 1))+
  coord_polar()

moritzlindner/ggped documentation built on Sept. 14, 2024, 12:14 p.m.