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