# `Pedixplorer`: a BioConductor package to create, filter and draw pedigree <!-- badges: start --> [](https://www.bioconductor.org/packages/Pedixplorer) [](https://www.bioconductor.org/packages/release/bioc/html/Pedixplorer.html#archives) [](http://bioconductor.org/packages/stats/bioc/Pedixplorer/) [](http://bioconductor.org/checkResults/devel/bioc-LATEST/Pedixplorer/) [](https://codecov.io/gh/LouisLeNezet/Pedixplorer) <!-- badges: end --> ||| |-|-| | This is a fork and the new version of the [**kinship2**](https://github.com/mayoverse/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. | <img src="https://github.com/LouisLeNezet/Pedixplorer/raw/devel/inst/figures/icon_Pedixplorer.png" align="right" max-height="140" style="align:center;max-height:200px;"/> | > Try today the [**Pedixplorer shiny app**](https://pedixplorer.univ-rennes.fr/) to easily use the package. ## Installation through R ### From Github ```R if (!require("remotes", quietly = TRUE)) install.packages("remotes") remotes::install_github("louislenezet/Pedixplorer", build_vignettes=TRUE ) ``` ### From Bioconductor ```R 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 how the affection and availability have to be draw are stored respectively in `scales$fill` and `scales$border` slots They are 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()` Method A Pedigreee `plot()` S4 method is available to plot the object 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](https://pedixplorer.univ-rennes.fr/).| <img src="https://github.com/LouisLeNezet/Pedixplorer/raw/devel/inst/figures/ShinyAppDiagram.png" alt="shiny-app_diagram" align="right" max-width="300" style="max-width:300px;align:right;"/>| ### Other Notable Functions * `useful_ind()` automatically find the individuals close to a given set of individuals, allowing to split the Pedigree in smaller family for an easier representation. * `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. ### Example Here is a simple example that show how to represent a complex pedigree with a lot of different information. ```R library(Pedixplorer) library(dplyr) data("sampleped") data("relped") # Create the Pedigree object pedi <- Pedigree(sampleped, relped, missid = NA) %>% generate_colors( # Add a new affection information col_aff = "num", is_num = TRUE, keep_full_scale = TRUE, breaks = 2, threshold = 3, colors_aff = c("#8B7355", "#FFA500"), colors_unaff = c("#8aca25", "#3fb7db") ) %>% is_informative( # Set which individuals are informative col_aff = "num", informative = "AvAf" ) %>% useful_inds( keep_infos = TRUE, # Keep available or affected parents max_dist = 2 # Maximum distance from informative individuals ) proband(ped(pedi)) <- isinf(ped(pedi)) # Set informative individuals as proband png("MyPedigree.png", width = 1000, height = 600) plot_list <- plot( pedi, symbolsize = 1.5, # Increase the symbole size title = "My pedigree", # Add a title legend = TRUE, # Add the legend leg_symbolsize = 0.02, # Set the symbole size of the legend leg_loc = c(0.5, 0.9, 0.8, 1.1), # Specify the legend location lwd = 0.5, # Set the line width ggplot_gen = TRUE, # Use ggplot2 to draw the Pedigree tips = c( "id", "avail", "affection", "num", "dateofbirth" ) # Add some information in the tooltip ) dev.off() # Plot the Pedigree with plotly to have an interactive plot plotly::ggplotly( plot_list$ggplot, tooltip = "text" ) %>% plotly::layout(hoverlabel = list(bgcolor = "darkgrey")) ``` <p align="center"> <img src="https://github.com/LouisLeNezet/Pedixplorer/raw/devel/inst/figures/MyPedigree.png" alt="MyPedigree" height="400" style="height:400px;"/> <br> <a href="https://louislenezet.github.io/assets/img/pedixplorer/pedigree_interactive.html" alt="MyPedigree">View Interactive Pedigree</a> </p> ## Documentation and News To view documentation start R and enter: ```R library(Pedixplorer) help(package="Pedixplorer") # Or to view the vignettes browseVignettes("Pedixplorer") # Or to see the news utils::news(package="Pedixplorer") ```