NEWS

---

Pedixplorer 1.7.1

• Fix slices in circfun()
• Add contributing guidelines
• Replace dplyr pipe %>% by |>

Pedixplorer 1.5.6

• Fix legend plotting when ggplot_gen is TRUE
• Reduce kindepth() warning and error messages to show necessary information.
• Fix lwd usage instead of cex in ped_to_legdf()

Pedixplorer 1.5.5

• Add label_cex and label_size to control id, date and label text position and size
• Fix csv reading with incoherent number of columns in rows
• Fix check box align_parents in ped_shiny()
• Fix auto_hint() error when couple present twice
• Fix stress computation when individual present more than twice
• Add ind_max_warning and ind_max_error for a better control of pedigree size to plot in shiny application

Pedixplorer 1.5.4

• Add best_hint computation to the shiny app and split it in different subfunction
• Remove little used library from Imports
• Change shinyWidgets::pickerInput to shiny::selectInput
• Remove 0 from default na_strings
• Update citation to use published article in Bioinformatics
• Add error for _ present in any id columns
• Fix shiny app notification title and slider intermediary value selection
• Fix full scale data reaffection on same column
• Improve position and size of proband label and assymptomatic symbol for logo

Pedixplorer 1.5.3

• Add short explanation of hints() usage in Pedigree alignment details vignette.

Pedixplorer 1.5.2

• Fix resizing plot in shiny module by adding dependency
• Update website and readme

Pedixplorer 1.5.1

• Separate plot management in a shiny module
• Add plot_resize shiny module
• Add help messages using shinyhelper
• Add plink_to_pedigree function to convert plink files to Pedigree object
• Add 0 as one of the default missing identifier value
• Set ggplot generation as independent without plotting on current device
• All draw_* functions return a layer instead of a ggplot object
• Add back message for individuals not plotted
• Add autocompletion of missing twins relationship with complete_twins()

Pedixplorer 1.3.4

• Add example of interactivness in vignette
• Fix label adjusting position in plot functions
• Fix arrow size in ggplot

Pedixplorer 1.3.1

• Add support for .ped, .tsv files in data import
• is_informative independent from useful_inds
• Use directly columns names from fill instead of the mods columns
• Move to R 4.4 and Bioc 3.20
• Fix unittests and update snapshots
• Change normalisation process to directly use id, dadid, momid, famid, sex no more need for indId, fatherId, ...
• affection is now used as default affection modality columns that will be used to generate affected
• status is replaced by deceased
• steril is replaced by fertility and corresponding symbols is added for infertile and infertile_choice_na
• terminated sex code is replace by miscarriage new slot
• miscarriage, evaluated, consultand, proband, carrier, asymptomatic and adopted are now recognize and use for plotting
• Argument order of Ped() as changed when using vectors. This choice has been made for a better consistency across the package. Please check that your argument are properly named (i.e. sex has been moved after famid and avail after deceased).
• Shiny application is updated and improved (aesthetics, errors, warnings, functionnalities).
• Add dateofbirth and dateofdeath to the Ped object
• Changee from round to signif for the precision argument
• Improve stability of test by adding and controlling the options() and par() arguments in the unittests.
• Carrier symbols is proportional to the mean of the box size

Pedixplorer 1.2.0

• Change code of ped_to_legdf
• When plotting with the main plot, the legend gets its own space separate from the plot. This allow better control over the size and localisation of the legend.
• The graphical parameters are reset after each use of plot_fromdf
• Add tooltips control in Pedigree plots and add it to the app
• Add example of interactivness in vignette
• Fix plot area function and legend creation for better alignment

Pedixplorer 1.1.4

• Update website and logo
• Improve ped_shiny() esthetics
• Change plot element order rendering for better looks
• Add more control to line width of box and lines
• Improve legend ordering
• Separate website building workflow from check
• Update function documentation and set to internal all unnecessary functions for users
• Stabilize unit test
• Standardize the vignettes and add more documentation
• Fix label adjusting position in plot functions

Pedixplorer 1.1.3

• Fix github workflows
• Disable ped_shiny() execution in markdown
• Publish with pkgdown

Pedixplorer 1.1.2

• Use R version 4.4 and update workflows

Pedixplorer 1.1.1

• A shiny application is now available through the ped_shiny() function.
• Function imports have been cleaned.
• Unit tests have been added as well as more snapshot to increase package coverage.
• relped dataset allows to easily test special relationship.
• Documentation is enhanced and correctly linted.
• precision parameter has been added to align4() and set_plot_area() to reduce noise between platform.
• fix_parents() has been fixed and improved.
• More controls over color setting with generate_colors().
• Possibility to force computation of alignement when it fails with force = TRUE.
• upd_famid_id() to upd_famid().
• Zooming in a pedigree object is now done by subsetting the dataframe computed by ped_to_plotdf().
• useful_inds() function has been improved.

Pedixplorer 0.99.0

• Kinship2 is renamed to Pedixplorer and hosted on Bioconductor.
• Pedigree is now a S4 object, all functions are updated to work with the new class
• Pedigree constructor now takes a data.frame as input for the Pedigree informations and for the special relationship. The two data.fram are normalized before being used.
• plot.pedigree support ggplot generation, mark and label can be added to the plot. The plot is now generated in two steps ped_to_plotdf() and plot_fromdf(). This allows the user to modify the plot before it is generated.
• All documentation are now generated with Roxygen
• New function available: generate_aff_inds, generate_colors, is_informative, min_dist_inf, normData, num_child, useful_inds
• All functions renamed to follow the snake_case convention
• All parameters renamed to follow the snake_case convention
• All test now use testthat files
• Vignettes have been updated to reflect the new changes