Pedixplorer: a BioConductor package to create, filter and draw pedigree

This is a fork and the new version of the kinship2 package. Initially a set of functions to view pedigrees while developing models that use kinship matrices, the functions were useful enough to put into a package of its own. It has now an S4 class for pedigrees, a kinship function that calculates the kinship matrix from a Pedigree object, and the Pedigree plotting routines that adhere to many of the standards for genetics counselors.

Try today the Pedixplorer shiny app to easily use the package.

Installation through R

From Github

if (!require("remotes", quietly = TRUE))
    install.packages("remotes")

remotes::install_github("louislenezet/Pedixplorer",
    build_vignettes=TRUE
)

From Bioconductor

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Pedixplorer")

Main functions

The Pedigree() Function

Pedigree() is a function that creates an S4 class Pedigree object. The core slot of the Pedigree object is the ped slot built from having a row per person, linked by the father id and mother id. Other relationships can be specified, and affection status can be a matrix of multiple categories in the rel slot. All the informations about affection and availability are be stored respectively in scales$fill and scales$border slots and are therefore used to fill and color the border for each elements of the Pedigree graph.

The generate_colors() Function

generate_colors() is a function that generates a color palette for an affection status. This function is used by the Pedigree() function to generate the scales$fill and scales$border slots. The user can also use this function to generate a color palette for a specific affection status that will be added to the Pedigree object.

The plot.Pedigree() Method

plot.Pedigree() is a method for a Pedigree object that plots as a "family tree", with relatives of the same generation on the same row, and affection statuses divided over the plot symbol for each person. This function is designed in two steps:

1. First the Pedigree object is converted into a data frame with all the elements needed to plot the Pedigree (i.e. boxes, lines, text, etc.). This is done by the ped_to_plotdf() function.
2. Then the data frame is plotted using the plot_fromdf() function.

The kinship() Funtion

kinship() is a function that creates the kinship matrix from a Pedigree object. It is coded for dyplotype organisms, handling all relationships that can be specified for the Pedigree object, including inbreeding, monozygotic twins, etc. A recent addition is handling the kinship matrix for the X and Y chromosomes.

The ped_shiny() Function

To help anyone to easily use all the main functions of the package a shiny app has been created, allowing you to import your data, normalise it, select the family and filter the resulting Pedigree object before visualising it. You'll also be able to download the resulting data and plot. The application is also available on a Virtual Machine accessible at pedixplorer.univ-rennes.

Other Notable Functions

• shrink() will shrink a Pedigree to a given size, keeping the most informative individuals for a single affection variable.

• fix_parents() will add parents for children who have a mother or dad listed that is not already included. It will also fix the sex status for the parent if it is mis-specified. This is useful to use before creating the Pedigree object.

Diagrams

The diagrams below show the main functions of the package and how they are related.

Details

Here is the details of the different parts of the diagram.

Process	Flow chart	Description
S4 Pedixplorer creation		The Pedigree S4 object creation is done by the Pedigree() constructor function. It mainly normalise a ped_df dataframe containing the information of each individuals with the norm_ped() function and the rel_df dataframe containing the special relationship (i.e. twins, spouse with no child) with the norm_rel() function. Thereafter It calls the generate_colors() function to create the colors scales (i.e. filling and border) before validating the object with is_valid()
Alignment		The alignment process is used to create a plist stroing the graphical disposition of the different individuals and their relation between them. The hints information used by auto_hint(), align() can be used by the user to force the ordering of some indiviuals
Plotting		The plotting process is now separated in three distinct steps: - ped_to_plotdf() is first called to convert the S4 Pedigree object into a dataframe listing all the graphical elements and their caracteristic. - ped_to_legdf() does the same but for the legend informations. - plot_fromdf() take as input such resulting dataframe and iteratively plot the elements based on their given characteristics. All those steps are merge in one step with the plot.Pedigree() method.
Shrinking		This process is useful when you want to reduce a huge Pedigree into a more simple version. The shrink() method will remove iteratively the less informative individuals from the Pedigree until it reach the max_bits size awaited
Informations		From a S4 Pedigree object it is possible to extract a lot of informations about the individuals, such as their shared relatedness kinship(), the number of direct and indirect child num_child(), their informativeness based on a set variable is_informative(), ...
Checking columns		The check_col() function is used to check the presence absence of columns in a designated data.frame
Legend		The diagrams listed here follow this rules

Documentation and News

To view documentation start R and enter:

library(Pedixplorer)
help(package="Pedixplorer")

# Or to view the vignettes
browseVignettes("Pedixplorer")

# Or to see the news
utils::news(package="Pedixplorer")