Added more flexibility to overlays, including support for shape-mode
overlays with custom numeric codes and colors.
Added a new vignette section to explain the clinical preset and its
features.
Add polar coordinates option to ggPedigree and
ggPedigreeInteractive
Enable support for adding variables to segments in ggPedigree and
ggPedigreeInteractive with the config setting of “reduce_variables”.
Setting this to FALSE allows for custom coloring, styling of segments,
and use of ggplot2’s aesthetics for segments. (Note: this is an advanced
feature that requires familiarity with ggplot2’s aesthetics and may not
be suitable for all users or datasets. It can be used to create more
customized and informative pedigree plots, but may require additional
configuration and testing to ensure that the segments are displayed
correctly. Use with caution and reach out to the maintainers if you have
questions or need assistance with this feature.)
Bug fixes
Fixed multi-overlay closure bug where all overlays were filtered on
the last column in the list due to R’s lazy evaluation of function
arguments. Local variable assignment now forces evaluation at the
correct loop iteration.
Fixed preset (e.g., "clinical") not being
forwarded to getDefaultPlotConfig() in
ggPedigree() and ggPedigreeInteractive(),
which meant preset-driven settings like
overlay_mode = "shape" and
overlay_include = TRUE were silently ignored.
Fixed tile_color_palette not being applied to ggRelatednessMatrix.
Instructions were out of date.
Fixed minor issues with ggRelatednessMatrix documentation and
examples.
Fixed minor issues with ggPhenotypebyDegree documentation and
examples.
ggpedigree Version: 1.1.1.1
Hotpatch to fix plotly vignette selectively failing by using
tryCatch to catch the error and print a warning instead of failing the
whole vignette build.
Also increased test coverage of kinship2_pedigree.
ggpedigree Version: 1.1.1.0
cran submission
Add scale label size by pedigree size option
Making the sexVar variable more robust
Add implemented CodeFactor recommendations for styling and
maintainability
ggpedigree 1.1.0.3
API notes
Documented ggPedigree() /
ggPedigreeInteractive() /
ggRelatednessMatrix() as canonical entry points while
retaining backward-compatible aliases.
New data
Added a preliminary Wars of the Roses pedigree dataset.
Improved dataset documentation.
Tweaked the GoT dataset example for improved clarity.
Split the squirrel dataset into smaller pedigrees for testing.
New features
Added a greyscale option to color_theme.
Added automatic point scaling based on pedigree size.
Added optional segment size scaling based on pedigree size.
Hid the Sex key by default in ggpedigree.
Added two vignettes describing ggpedigree configuration
options.
Cross-referenced vignettes in function documentation.
Validation and messages
Performed required-column checks earlier in
ggpedigree(), including sex.
Improved errors for invalid or non-standard sex
coding.
Improved the warning message used in tryCatch().
Made code_male handling more resilient when using
config values.
Bug fixes
Standardized naming by replacing midparent with
mid_parent.
Fixed inconsistent handling of character vs numeric IDs.
Internal changes
Changed default colors and sizes for better visibility.
Saved raw Excel inputs as CSV for non-proprietary storage.
Refactored kinship2 internals for maintainability.
Refactored node-adding internals.
Remove reshape2 dependency
Deprecating plotPedigree function in favor of
kinship2_plotPedigree
Testing
Expanded tests for ID and sex-code inputs, including type,
missingness, and configuration scenarios.
ggpedigree 1.0.0.1
cran resubmission
Fixed a minor documentation issue with a URL whose certificate had
expired.
ggpedigree 1.0.0
cran submission
Integrated kinship2 functions to remove the dependency
Made kinship2 package optional, required for plotPedigree (a
kinship2 wrapper)
Importing relevant tests from kinship2 package
Updated documentation to reflect changes
Refactored code to improve maintainability
Added more unit tests for the new functions
Add max_message_n to pedigree function to allow users to get more
messages about pedigree complexity
ggpedigree 0.9.1
Minor documentation revisions to complement JOSS paper update
Added test coverage for buildSpouseSegments
ggpedigree 0.9.0
cran release
smarter segment coloring
added setting to hide legend for sex
avoided sapply() in ggPedigreeInteractive
added subfunction for adding twins
add non-dot versions of internal functions for evaluating
complexity
added alpha settings
added compatibility with pedigree objects from kinship2
exposed code_female, code_na to config
added tests for kinship2 compatibility
Updated JOSS paper
Refactored step 2+3 of the ggpedigree function to
.transformPed()
Renamed p variable as plotObject in ggpedigree subfunctions
Smarter implementation of aliases
Updated hex to actually use ggpedigree
Exposed ‘relations’ and ‘hints’ inputs to ggpedigree
Added more intuitive defaults
refactor calcCoordinates with alignPedigreeWithHints and
alignPedigreeWithRelations
Vectorized part of calcCoordinates
removed redundant plotPedigree verbose section
add log2 option for relatedness
Improve plotly conversion
ggpedigree 0.8.0
joss paper submitted
Makes ggrepel a suggested package instead of a required one.
Make connections included in the plot by default.
Expose linejoin in ggRelatednessMatrix
Expose outline_additive and outline_alpha to ggpedigree
Refactored the ggpedigree function to improve readability and
maintainability.
Transferring ASOIAF data from BGmisc to ggpedigree
ggpedigree 0.7.1
Fixed focal_fill ID indexing to row order instead of ID order.
Fixed bug in using fam_x and fam_y in with generation_height
Add option to add phantom parents to the pedigree plot.
Alerts when duplicate or bad configs appear
Make palleter suggested instead of required
ggpedigree 0.7.0
Changed the default behavior of ggPedigree to use x_fam
and y_fam for positioning families, rather than x_mid_parent and
y_mid_parent. This change improves visualization of pedigrees with many
families.
Changed the get midpoint of curvature to better approximate
geom_curv behavior.
reduced redundancy in code base by not calculating the parent
midpoints when not needed.
Added default_config support for ggRelatednessMatrix functions.
ggpedigree 0.6.1
Transferred plotPedigree() function from BGmisc to
ggpedigree.
ggpedigree 0.6.0
Implemented fill by matID, patID using various scales, such as hue,
viridis, and others.
Added support for emojis in the ggpedigree
function.
Solved the bug that created excessive branches
Made the twin sibling segments smarter
Adding more debug support
ggpedigree 0.5.1
Fix tooltip appearing in ggPedigreeInteractive when
tooltip_include is FALSE.
ggpedigree 0.5.0
Added segment_linetype and custom affected labels to the
ggpedigree function.
Added usage of color_palette to the ggpedigree
function.
Added curvature option to the ggpedigree function.
Add support for custom affected labels for affected individuals in
the ggpedigree function.
Add support for removing diagonal, upper triangle, and lower
triangle in the ggRelatednessMatrix function.
Add support for labeling tiles
Added new tests for the ggRelatednessMatrix
function.
Added new phenotype plotting function
ggPhenotypebyDegree to visualize phenotypes by degree of
relatedness.
Added new vignette to explain ggPhenotypebyDegree.
Added a new function getDefaultPlotConfig to set
default configuration options for the package.
Harmonized the configuration options across the package to use
getDefaultPlotConfig and buildPlotConfig
Added unit tests for getDefaultPlotConfig and
ggPhenotypebyDegree
Added workaround for plotly non-support for geom_curve with
computeCurvedMidpoint
Adding fully twin plotting features
Added ability to fill colors as a function of the degree of
relatedness to a focal person
Add getDefaultPlotConfig functionality to ggPhenotypebyDegree
Fully documented getDefaultPlotConfig so that each config option is
clear and understandable.
ggpedigree 0.4.1
Status: Submitted to CRAN
Fixed a bug in the ggpedigree function that caused an
error when using a custom ID name and requesting the plot as a ggplot
object.
ggpedigree 0.4.0
Allows support for character-based IDs
Added linejoin, lineend, segment_self_linetype, option to the
ggpedigree functions.
Added unit tests for calculateConnections and ggpedigree
functions.
Refactored ggpedigree function into ggpedigree.core and .addScales
and .addLabels functions to improve readability and
maintainability.
Renamed symKey to makeSymmetricKey, extended it to support
character-based IDs, and added unit tests.
Added a new function ggPedigreeInteractive to create
interactive pedigree plots using plotly. Added a vignette
to show its usage.
Added redsquirrels dataset to the package for testing and
examples.
Added a new function ggRelatednessMatrix and
subfunction ggRelatednessMatrix.core to create heatmaps of
relatedness matrices.
Added new vignette to explain ggRelatednessMatrix
Added graphic tests for ggpedigree,
ggPedigreeInteractive, and ggRelatednessMatrix
functions.
Updated the README and vignettes to reflect the new features and
improvements.
Updated description to meet CRAN policies.
ggpedigree 0.3.0
Expose more labeling options in the ggpedigree function
to allow for more customization, including nudging labels, and changing
the variable used.
Added option to add an outline to the pedigree plot.
Made the config options more consistent and user-friendly.
Enhance the narrative of the plotting vignette to explain the new
features and provide clearer examples.
Added missing examples to the ggpedigree function
documentation.
ggpedigree 0.2.0
Extended functionality to include new plotting features, like
handling repeated instances of the same individual in a pedigree.
Improved documentation and examples for better user guidance.
Added unit tests for describeHelpers
ggpedigree 0.1.0
Implemented pedigree plotting functions for
ggplot2.
Added vignette to explain the use of the package in basic
plotting.
Created a DESCRIPTION file to define the package and
its dependencies.
Added a LICENSE file to specify the terms under which
the package applies.
Created a CODE_OF_CONDUCT.md file to outline the
expected behavior of contributors and maintainers.
Added a NEWS.md file to track changes to the
package.
Created a CONTRIBUTING.md file to guide contributors on
how to contribute to the package.
Added a README.Rmd file to provide an overview of the
package and its functions.
Added a cran-comments.md file to document the
submission process to CRAN.