Changelog • Pedixplorer

Changes in v1.3.1

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

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

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

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.

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