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ggpedigree: Plotting tool for simple and complex pedigrees.

Source: R/ggpedigree.R
ggpedigree.Rd

This function plots simple and complex pedigrees, with options specific to the types of pedigrees used for quantitative genetic inference in natural populations. This function is flexible to missing parents and can be customized to visualise specific cohorts, sexes, and/or phenotype availability. Pedigree layout is optimized using a Sugiyama algorithm. For simpler pedigrees, visualisation may be improved by specifying spread_x_coordinates = FALSE.

Usage

ggpedigree(
  .data,
  ids,
  mothers,
  fathers,
  cohort,
  sex,
  pheno,
  sex_code = NULL,
  id_labels = FALSE,
  remove_singletons = TRUE,
  plot_unknown_cohort = FALSE,
  spread_x_coordinates = TRUE,
  print_cohort_labels = TRUE,
  return_plot_tables = FALSE,
  line_col_mother = "#E41A1C",
  line_col_father = "#377EB8",
  line_col_no_pheno = "#aaaaaa",
  line_alpha = 0.3,
  point_size = 1,
  point_colour = "black",
  point_alpha = 1
)

Arguments

.data

a data frame object with all the pedigree information

ids

a column of .data of individual identifiers

mothers

A column of .data of mothers corresponding to ids. Missing values are 0 or NA.

fathers

A column of .data of fathers corresponding to ids. Missing values are 0 or NA.

cohort

integer. Default NULL. A optional column of .data assigning a cohort to each id. If NULL, then kinship2::kindepth is used to assign cohorts to ids.

sex

integer or character. Default NULL. An optional column of .data assigning a sex to each id. When using this option, sex_code must be specified. Any values not matching values in sex_code will be treated as unknown sex.

pheno

integer or character. Default NULL. An optional column of .data assigning a phenotype to each id. Links originating from parents that have NA values for this argument will be plotted with a grey line, unless otherwise specified in line_col_no_pheno.

sex_code

Default NULL. A vector of length 2, indicating the value used in sex for females and males respectively. Females are plotted as circles, males as squares, and unknown values as triangles.

id_labels

logical. Default FALSE. Print the ids on the pedigree plot.

remove_singletons

logical. Default TRUE. Remove ids with no relatives i.e., no offspring or parents assigned.

plot_unknown_cohort

logical. Default FALSE. Plots ids of unknown cohorts. These are plotted in an "Unknown" cohort at the top of the pedigree. Be aware that any mothers and fathers of these individuals will be plotted below them.

spread_x_coordinates

logical. Default TRUE. Evenly spreads the x-axis (horizontal) distribution of points within each cohort. If FALSE, this will plot the direct outcome of igraph::layout_with_sugiyama; the FALSE option is only recommended for small pedigrees and/or less connected pedigrees.

print_cohort_labels

logical. Default TRUE. Prints cohort levels on the left hand side of plot.

return_plot_tables

logical. Default FALSE. Returns an object with the line and point data used for the plot, but the plot will not be generated

line_col_mother

Default = "#E41A1C". Line colour for maternal links.

line_col_father

Default = "#377EB8". Line colour for paternal links.

line_col_no_pheno

Default = "#aaaaaa". Line colour for parents with NA values in pheno.

line_alpha

Default = 0.3. Line alpha (transparency) value for maternal and paternal links.

point_size

Default = 1. Point size for ids.

point_colour

Default = "black". Point colour for ids.

point_alpha

Default = 1. Point alpha for ids.

Value

output a ggplot object or a list of tables if return_plot_tables = TRUE

Examples

data(gryphons)
pedigree <- fix_ped(gryphons[, 1:3])

## draw the gryphon pedigree by pedigree depth
ggpedigree(pedigree)
#> Warning: the first 3 columns were used for id, dam and sire identity, please specify if not correct or to remove the warning


# \donttest{
# specifying the column names for id, mother and father
ggpedigree(pedigree, id, dam, sire)


# with cohort and sex
ggpedigree(gryphons, cohort = cohort, sex = sex, sex_code = c(1, 0))
#> Warning: the first 3 columns were used for id, dam and sire identity, please specify if not correct or to remove the warning


#' with cohort, sex, and pheno
gryphons$pheno <- 1
gryphons$pheno[sample(length(gryphons$pheno), 1000)] <- NA
ggpedigree(gryphons, cohort = cohort, sex = sex, sex_code = c(1, 0), pheno = pheno)
#> Warning: the first 3 columns were used for id, dam and sire identity, please specify if not correct or to remove the warning

# }