Tidying and visualization for animal pedigrees.
The visPedigree package provides tools to check for duplicate and bisexual individuals, detect pedigree loops, add missing founders, sort parents before offspring, and trace the pedigrees of specified candidates. It generates hierarchical graphs for all individuals in a pedigree and can handle very large datasets (> 10,000 individuals per generation) by compacting full-sib groups. It is particularly effective for aquatic animal pedigrees, which often include numerous full-sib families per generation in nucleus breeding populations.
More complex pedigree graphs can be found in the vignettes.
(Note: The package is preparing for submission and not yet available on CRAN)
# install.packages("visPedigree")You can install the development version from GitHub using the devtools package:
# install.packages("devtools")
devtools::install_github("luansheng/visPedigree")library(visPedigree)
# Example 1: Tidy and visualize a small pedigree
# Draw the pedigree, compacting full-sib individuals and highlighting candidates.
# Note: the compacted candidates are also highlighted here.
cands <- c("Y", "Z1", "Z2")
small_ped |>
tidyped(cand = cands) |>
visped(compact = TRUE, highlight = cands)
# Example 2: Calculate and show inbreeding coefficients
library(data.table)
data.table(
Ind = c("A", "B", "C", "D", "E"),
Sire = c(NA, NA, "A", "C", "C"),
Dam = c(NA, NA, "B", "B", "D"),
Sex = c("male", "female", "male", "female", "male")
) |>
tidyped(inbreed = TRUE) |>
visped(highlight = c("E"), showf = TRUE)
# Example 3: Summarize pedigree statistics
# Get a quick overview of the pedigree structure
small_ped |>
tidyped() |>
summary()
Drawing an animal pedigree using the visPedigree package EN CN
LUAN Sheng (2018). visPedigree: A package for tidying and drawing animal pedigree. URL https://github.com/luansheng/visPedigree.