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# The `Pedixplorer` Package <img src="./inst/figures/icon_Pedixplorer.png" align="right" height="139" /> [![CRAN_Status_Badge](]( [![Downloads](]( [![Total-Downloads](]( 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. ## Installation ### From Github To install this package from Github you can use the following R script: ```R if (!require("remotes", quietly = TRUE)) install.packages("remotes") remotes::install_github("louislenezet/Pedixplorer", build_vignettes=TRUE ) ```` ### From Bioconductor (not yet available) To install this package you can use the following R script: ```R if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Pedixplorer") ``` ## Documentation To view documentation for the version of this package installed in your system, start R and enter: ```R browseVignettes("Pedixplorer") ``` ## News To see the new functions / modification please use: ```R utils::news(package="Pedixplorer") ``` ## The 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. ### 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. ![Pedixplorer Diagram](./inst/figures/Pedixplorer_diagram.png) ### Details Here is the details of the different parts of the diagram. | Process | Flow chart | Description | |:---------------------|:--------------------------:|----------------------| | **S4 Pedixplorer creation** | <img src="inst/figures/pedigreeobj.png" alt="pedigreeobj" width="800"/> | 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** | <img src="inst/figures/alignment.png" alt="alignment" width="800"/> | 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** | <img src="inst/figures/plotting.png" alt="plotting" width="800"/> | The plotting process is now separated in three distinct steps: <br> - **ped_to_plotdf()** is first called to convert the *S4 Pedigree object* into a dataframe listing all the graphical elements and their caracteristic. <br> - **ped_to_legdf()** does the same but for the legend informations. <br> - **plot_fromdf()** take as input such resulting dataframe and iteratively plot the elements based on their given characteristics. <br> All those steps are merge in one step with the **plot.Pedigree()** method. | | **Shrinking** | <img src="inst/figures/shrinking.png" alt="shrinking" width="800"/> | 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** | <img src="inst/figures/infos.png" alt="infos" width="800"/> | 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** | <img src="inst/figures/checkingcol.png" alt="checkingcol" height="200"/> | The **check_col()** function is used to check the presence absence of columns in a designated *data.frame* | | **Legend** | <img src="inst/figures/legend.png" alt="legend" height="200"/> | The diagrams listed here follow this rules |