Centralized configuration list used by all gg-based plotting functions. Returns a named list of default settings used by all gg-based plotting functions. This configuration can be overridden by supplying a list of key-value pairs to plotting functions such as `ggPedigree()`, `ggRelatednessMatrix()`, and `ggPhenotypeByDegree()`. Each key corresponds to a configurable plot, layout, or aesthetic behavior.
Usage
getDefaultPlotConfig(
function_name = "getDefaultPlotConfig",
personID = "personID",
status_column = NULL,
alpha_default = 1,
apply_default_scales = TRUE,
apply_default_theme = TRUE,
segment_default_color = "black",
color_theme = "color",
greyscale_palette_default = c("grey10", "grey50", "grey85"),
greyscale_low = "black",
greyscale_mid = "grey50",
greyscale_high = "white",
color_palette_default = c("#440154FF", "#7fd34e", "#f1e51d"),
color_palette_low = "#000004FF",
color_palette_mid = "#56106EFF",
color_palette_high = "#FCFDBFFF",
color_scale_midpoint = 0.5,
color_scale_theme = "ggthemes::calc",
alpha = alpha_default,
plot_title = NULL,
plot_subtitle = NULL,
value_rounding_digits = 5,
code_male = 1,
code_na = NA,
code_unknown = NULL,
code_female = 0,
label_include = TRUE,
label_column = "personID",
label_method = "geom_text",
label_max_overlaps = 25,
label_nudge_x = 0,
label_nudge_y = 0.15,
label_nudge_y_flip = TRUE,
label_segment_color = NA,
label_text_angle = 0,
label_text_size = 3,
label_text_color = "black",
label_text_family = "sans",
label_scale_by_pedigree = TRUE,
point_size = 6,
point_scale_by_pedigree = TRUE,
outline_include = FALSE,
outline_multiplier = 1.25,
outline_additional_size = 0,
outline_alpha = 1,
outline_color = "black",
tooltip_include = TRUE,
tooltip_columns = c("ID1", "ID2", "value"),
axis_x_label = NULL,
axis_y_label = NULL,
axis_text_angle_x = 90,
axis_text_angle_y = 0,
axis_text_size = 9,
axis_text_color = "black",
axis_text_family = "sans",
generation_height = 1,
generation_width = 1,
ped_packed = TRUE,
ped_align = TRUE,
ped_width = 15,
fast_threshold = 1000,
founder_order_seed = NULL,
founder_order_tries = 1L,
layout_score_method = "composite",
fixed_positions = NULL,
fixed_positions_update_family = TRUE,
coord_layout = "cartesian",
coord_radial_start_angle = -90,
coord_radial_end_angle = 270,
coord_radial_scale = 1.5,
coord_radial_min_radius = 0.75,
spread_out_generations = TRUE,
spread_out_generations_factor = 0.5,
segment_linewidth = 0.8,
segment_linetype = 1,
segment_lineend = "round",
segment_linejoin = "round",
segment_scale_by_pedigree = FALSE,
segment_offspring_color = segment_default_color,
segment_parent_color = segment_default_color,
segment_self_color = segment_default_color,
segment_sibling_color = segment_default_color,
segment_spouse_color = segment_default_color,
segment_spouse_alpha = if (segment_lineage_legend_show) 0.5 else 1,
segment_mz_color = segment_default_color,
segment_mz_linetype = segment_linetype,
segment_mz_alpha = 1,
segment_mz_t = 0.6,
segment_self_linetype = "dotdash",
segment_self_linewidth = 0.5 * segment_linewidth,
segment_self_alpha = 0.5,
segment_self_angle = 90,
segment_self_curvature = -0.2,
segment_lineage_include = FALSE,
segment_lineage_component = "mitochondrial",
segment_lineage_focal_personID = NULL,
segment_lineage_types = c("parent", "offspring", "sibling", "mz", "spouse"),
segment_lineage_method = "viridis_d",
segment_lineage_palette = focal_fill_color_values,
segment_lineage_na_color = "grey80",
segment_lineage_force_zero = TRUE,
segment_lineage_legend_show = segment_lineage_include,
segment_lineage_legend_title = "Lineage",
sex_color_include = TRUE,
sex_legend_title = "Sex",
sex_shape_labels = c("Female", "Male", "Unknown"),
sex_color_palette = color_palette_default,
sex_shape_female = 16,
sex_shape_male = 15,
sex_shape_unknown = 18,
sex_shape_values = NULL,
sex_shape_include = TRUE,
sex_legend_show = FALSE,
status_include = TRUE,
status_code_affected = 1,
status_code_unaffected = 0,
status_label_affected = "Affected",
status_label_unaffected = "Unaffected",
status_alpha_affected = 1,
status_alpha_unaffected = 0,
status_color_palette = c(color_palette_default[1], color_palette_default[2]),
status_color_affected = "black",
status_color_unaffected = color_palette_default[2],
status_shape_affected = 4,
status_legend_title = "Affected",
status_legend_show = FALSE,
overlay_shape = 4,
overlay_code_affected = 1,
overlay_code_unaffected = 0,
overlay_label_affected = "Affected",
overlay_label_unaffected = "Unaffected",
overlay_alpha_affected = 1,
overlay_alpha_unaffected = 0,
overlay_color = "black",
overlay_include = FALSE,
overlay_mode = "alpha",
overlay_size = NULL,
overlay_stroke = 1.5,
overlay_legend_title = "Overlay",
overlay_legend_show = FALSE,
focal_fill_include = FALSE,
focal_fill_legend_show = TRUE,
focal_fill_personID = 1,
focal_fill_legend_title = "Focal Fill",
focal_fill_high_color = "#FDE725FF",
focal_fill_mid_color = "#9F2A63FF",
focal_fill_low_color = "#0D082AFF",
focal_fill_scale_midpoint = color_scale_midpoint,
focal_fill_method = "gradient",
focal_fill_component = "additive",
focal_fill_n_breaks = NULL,
focal_fill_na_color = "black",
focal_fill_shape = 21,
focal_fill_force_zero = FALSE,
focal_fill_use_log = FALSE,
focal_fill_hue_range = c(0, 360),
focal_fill_chroma = 50,
focal_fill_lightness = 50,
focal_fill_hue_direction = "horizontal",
focal_fill_viridis_option = "D",
focal_fill_viridis_begin = 0,
focal_fill_viridis_end = 1,
focal_fill_viridis_direction = 1,
focal_fill_color_values = c("#052f60", "#e69f00", "#56b4e9", "#009e73", "#f0e442",
"#0072b2", "#d55e00", "#cc79a7"),
focal_fill_labels = c("Low", "Mid", "High"),
filter_n_pairs = 500,
filter_degree_min = 0,
filter_degree_max = 7,
drop_classic_kin = FALSE,
drop_non_classic_sibs = TRUE,
use_only_classic_kin = TRUE,
use_relative_degree = TRUE,
group_by_kin = TRUE,
match_threshold_percent = 10,
max_degree_levels = 12,
grouping_column = "mtdna_factor",
annotate_include = TRUE,
annotate_x_shift = -0.1,
annotate_y_shift = 0.005,
ci_include = TRUE,
ci_ribbon_alpha = 0.3,
tile_color_palette = c("white", "gold", "red"),
tile_interpolate = TRUE,
tile_color_border = NA,
tile_cluster = TRUE,
tile_geom = "geom_tile",
tile_na_rm = FALSE,
tile_linejoin = "mitre",
matrix_fill_legend_title = "Relatedness",
matrix_diagonal_include = TRUE,
matrix_upper_triangle_include = FALSE,
matrix_lower_triangle_include = TRUE,
matrix_sparse = FALSE,
matrix_isChild_method = "partialparent",
return_static = TRUE,
return_widget = FALSE,
return_interactive = FALSE,
return_mid_parent = FALSE,
reduce_variables = TRUE,
reposition_founders = TRUE,
return_best_seed = FALSE,
hints = NULL,
relation = NULL,
debug = FALSE,
override_many2many = FALSE,
optimize_plotly = TRUE,
recode_missing_ids = TRUE,
recode_missing_sex = TRUE,
add_phantoms = FALSE,
affected_fill_include = FALSE,
affected_fill_code_affected = 1,
affected_fill_code_unaffected = 0,
affected_fill_label_affected = "Affected",
affected_fill_label_unaffected = "Unaffected",
affected_fill_color_affected = "black",
affected_fill_color_unaffected = NA,
affected_fill_shape_female = 21,
affected_fill_shape_male = 22,
affected_fill_shape_unknown = 23,
outline_color_include = FALSE,
outline_color_code_affected = 1,
outline_color_code_unaffected = 0,
outline_color_label_affected = "Highlighted",
outline_color_label_unaffected = "Default",
outline_color_affected = "blue",
outline_color_unaffected = "black",
preset = "none",
...
)Arguments
- function_name
The name of the function calling this configuration.
- personID
The column name for person identifiers in the data.
- status_column
The column name for affected status in the data.
- alpha_default
Default alpha transparency level.
- apply_default_scales
Whether to apply default color scales.
- apply_default_theme
Whether to apply default ggplot2 theme.
- segment_default_color
A character string for the default color of segments in the plot.
- color_theme
Theme mode controlling default palettes. Options: "color" (default) or "greyscale".
- greyscale_palette_default
Default discrete greyscale palette used when color_theme="greyscale".
- greyscale_low
Greyscale low color for continuous gradients when color_theme="greyscale".
- greyscale_mid
Greyscale midpoint color for continuous gradients when color_theme="greyscale".
- greyscale_high
Greyscale high color for continuous gradients when color_theme="greyscale".
- color_palette_default
A character vector of default colors for the plot.
- color_palette_low
Color for the low end of a gradient.
- color_palette_mid
Color for the midpoint of a gradient.
- color_palette_high
Color for the high end of a gradient.
- color_scale_midpoint
Midpoint value for continuous color scales.
- color_scale_theme
Name of the color scale used (e.g., "ggthemes::calc").
- alpha
Default alpha transparency for plot elements.
- plot_title
Main title of the plot.
- plot_subtitle
Subtitle of the plot.
- value_rounding_digits
Number of digits to round displayed values.
- code_male
Integer/string code for males in data. Default is 1.
- code_na
optional Integer/string code for missing values in data. Default is NA.
- code_unknown
optional Integer/string code for unknown sex in data. Default is NULL.
- code_female
optional Integer/string code for females in data. Default is 0.
- label_include
Whether to display labels on plot points.
- label_column
Column to use for text labels.
- label_method
Method used for labeling (e.g., ggrepel, geom_text).
- label_max_overlaps
Maximum number of overlapping labels.
- label_nudge_x
Horizontal nudge for label text.
- label_nudge_y
Vertical nudge for label text.
- label_nudge_y_flip
TRUE. Whether to flip the nudge y value to be negative. The plot is reversed vertically, so this is needed to nudge labels up instead of down.
- label_segment_color
Segment color for label connectors.
- label_text_angle
Text angle for labels.
- label_text_size
Font size for labels.
- label_text_color
Color of the label text.
- label_text_family
Font family for label text.
- label_scale_by_pedigree
Whether to scale label size by pedigree size.
- point_size
Size of points drawn in plot.
- point_scale_by_pedigree
Whether to scale point sizes by pedigree size.
- outline_include
Whether to include outlines around points.
- outline_multiplier
Multiplier to compute outline size from point size.
- outline_additional_size
Additional size added to outlines.
- outline_alpha
Alpha transparency for point outlines.
- outline_color
Color used for point outlines.
- tooltip_include
Whether tooltips are shown in interactive plots.
- tooltip_columns
Columns to include in tooltips.
- axis_x_label
Label for the X-axis.
- axis_y_label
Label for the Y-axis.
- axis_text_angle_x
Angle of X-axis text.
- axis_text_angle_y
Angle of Y-axis text.
- axis_text_size
Font size of axis text.
- axis_text_color
Color of axis text.
- axis_text_family
Font family for axis text.
- generation_height
Vertical spacing of generations.
- generation_width
Horizontal spacing of generations.
- ped_packed
Whether the pedigree should use packed layout.
- ped_align
Whether to align pedigree generations.
- ped_width
Plot width of the pedigree block.
- fast_threshold
Threshold for switching to piecewise layout algorithms for large pedigrees.
- founder_order_seed
Integer seed used to shuffle the pedigree row order before passing to kinship2. Because kinship2 processes founders in the order they appear, different shufflings produce different lateral placements. Set to an integer (e.g. `42`) to get a specific alternative layout. `NULL` (default) uses the original row order. Combine with `founder_order_tries` to search automatically for a compact layout.
- founder_order_tries
Integer number of row-order shufflings to evaluate. When greater than 1, the function tries seeds
founder_order_seed + 0, founder_order_seed + 1, ...(or1, 2, ...whenfounder_order_seedisNULL), scores each layout with `layout_score_method`, and returns the best result. Default is1(no search).- layout_score_method
Scoring method used to rank candidate layouts when `founder_order_tries > 1`. One of:
- `"parent_stub"`
(default) Sum of `|x_fam - x_pos|`. Total diagonal parent-stub length.
- `"crossings"`
Count of crossing parent-stub segment pairs within each generation.
- `"duplications"`
Count of extra kinship2 duplicate placements (`extra = TRUE` rows).
- `"twin_penalty"`
Sum of intruder positions separating co-twins within their generation row. Twins placed in different generation rows receive a heavy flat penalty.
- `"composite"`
Weighted sum: `parent_stub + 10*crossings + 20*twin_penalty + 100*duplications`.
Lower scores are better in all cases.
- fixed_positions
Optional data frame for pinning specific individuals to exact layout slots, overriding the computed layout. It must contain an ID column named to match `personID` (e.g., `"personID"` or `"ID"`) plus an `x` and/or `y` column. Each row sets that person's absolute position in raw layout-slot units (the units `calculateCoordinates()` emits, before `generation_width`/`generation_height` scaling and any radial transform). A missing or `NA` axis leaves the computed value unchanged. IDs not found in the pedigree are ignored with a warning. Default is `NULL` (no pinning).
- fixed_positions_update_family
When pinning a parent, whether to recompute the family anchor (`x_fam`/`y_fam`) of that parent's children so the parent-to-children connector follows the pinned parent. `TRUE` (default) keeps connectors attached; `FALSE` moves only the node and spouse link, leaving the down-connector at the original location. Has no effect when nothing is pinned.
- coord_layout
Layout mode for the pedigree. Options: "cartesian" (default) or "radial".
- coord_radial_start_angle
Start angle in degrees for the radial layout (default: -90, placing the first generation at the top).
- coord_radial_end_angle
End angle in degrees for the radial layout (default: 270, completing a full circle back to the top).
- coord_radial_scale
Radius increment per generation unit in the radial layout (default: 1.5).
- coord_radial_min_radius
Minimum radius offset for the innermost generation ring in radial layout (default: .75). Prevents the innermost generation from collapsing to the center of the circle where nodes would overlap. Increase this value to add more space at the center.
- spread_out_generations
Whether to apply a multiplicative spread factor to generation spacing in radial layout. Default is TRUE.
- spread_out_generations_factor
Multiplicative spread factor used in
.applyRadialLayoutto push outer generations further from the center (default: 0.5).- segment_linewidth
Line width for segments. Default is 0.80.
- segment_linetype
Line type for segments. Default is 1 (solid).
- segment_lineend
Line end type for segments. Default is "round".
- segment_linejoin
Line join type for segments. Default is "round".
- segment_scale_by_pedigree
Whether to scale segment sizes by pedigree size. Default is FALSE.
- segment_offspring_color
Color for offspring segments. Default uses segment_default_color.
- segment_parent_color
Color for parent segments. Default uses segment_default_color.
- segment_self_color
Color for self-loop segments. Default uses segment_default_color.
- segment_sibling_color
Color for sibling segments. Default uses segment_default_color.
- segment_spouse_color
Color for spouse segments. Default uses segment_default_color.
- segment_spouse_alpha
Alpha for spouse segments. Default is 1 when segment filling is disabled, and 0.5 when enabled.
- segment_mz_color
Color for monozygotic twin segments. Default uses segment_default_color.
- segment_mz_linetype
Line type for MZ segments. Default uses segment_linetype.
- segment_mz_alpha
Alpha for MZ segments. Default is 1.
- segment_mz_t
Tuning parameter for MZ segment layout. Default is 0.6.
- segment_self_linetype
Line type for self-loop segments. Default is "dotdash".
- segment_self_linewidth
Width of self-loop segment lines. Default is half of segment_linewidth.
- segment_self_alpha
Alpha value for self-loop segments. Default is 0.5.
- segment_self_angle
Angle of self-loop segment. Default is 90 degrees.
- segment_self_curvature
Curvature of self-loop segment. Default is -0.2.
- segment_lineage_include
Whether to color segments by family lineage (e.g., paternal, maternal, or mitochondrial lines). When `FALSE` (default), segments use the fixed per-type colors. When `TRUE`, participating segments are colored by a `segment_lineage` value derived from `segment_lineage_component`.
- segment_lineage_component
Which lineage to trace. Uses the same vocabulary as `focal_fill_component`: `"mitochondrial"`/`"mtdna"`, `"additive"`, `"common nuclear"`, `"maternal"`, `"paternal"`, or `"family"`. Default is `"mitochondrial"`.
- segment_lineage_focal_personID
Optional ID of a focal person. When supplied, segments are colored by their lineage relationship *to that person* (off-line segments become `NA`/grey), letting you trace the lines connected to one node. When `NULL` (default), partition components (`maternal`, `paternal`, `family`, `mitochondrial`) color segments by their own lineage group, while continuous relatedness components (`additive`, `common nuclear`) color relative to a default reference person (`focal_fill_personID`).
- segment_lineage_types
Character vector of segment types that participate in lineage coloring. Any of `"spouse"`, `"parent"`, `"offspring"`, `"sibling"`, `"mz"`. Default is `c("parent", "offspring", "sibling", "mz")` (the inheritance-bearing segments). Self-loop segments always keep their fixed color.
- segment_lineage_method
Scale method for the segment lineage color aesthetic. One of `"viridis_d"`, `"viridis_c"`, `"viridis_b"`, `"hue"`, `"manual"`, `"gradient"`, `"gradient2"`, `"steps"`. Default is `"viridis_d"`.
- segment_lineage_palette
Optional vector of colors for `segment_lineage_method = "manual"`.
- segment_lineage_na_color
Color used for segments with no lineage value (off-line or non-participating). Default is `"grey80"`.
- segment_lineage_force_zero
When using a focal person with a continuous component (e.g., mitochondrial/additive), replace `0` relationships with `NA` so off-line segments are greyed out. Default is `TRUE`.
- segment_lineage_legend_show
Whether to show the segment lineage legend. Default is TRUE.
- segment_lineage_legend_title
Title for the segment lineage legend. Default is "Lineage".
- sex_color_include
Whether to color nodes by sex. Default is TRUE.
- sex_legend_title
Title of the sex legend.
- sex_shape_labels
Labels used in sex legend.
- sex_color_palette
A character vector of colors for sex. Default uses color_palette_default.
- sex_shape_female
Shape for female nodes. Default is 16 (circle).
- sex_shape_male
Shape for male nodes. Default is 15 (square).
- sex_shape_unknown
Shape for unknown sex nodes. Default is 18 (diamond).
- sex_shape_values
A named vector mapping sex codes to shapes.
- sex_shape_include
Whether to display the shape for sex variables
- sex_legend_show
Whether to display sex in the legend or not.
- status_include
Whether to display affected status.
- status_code_affected
Value that encodes affected status.
- status_code_unaffected
Value that encodes unaffected status.
- status_label_affected
Label for affected status.
- status_label_unaffected
Label for unaffected status.
- status_alpha_affected
Alpha for affected individuals.
- status_alpha_unaffected
Alpha for unaffected individuals. Default is 0 (transparent).
- status_color_palette
A character vector of colors for affected status.
- status_color_affected
Color for affected individuals.
- status_color_unaffected
Color for unaffected individuals.
- status_shape_affected
Shape for affected individuals.
- status_legend_title
Title of the status legend.
- status_legend_show
Whether to show the status legend.
- overlay_shape
Shape used for overlaying points in the plot. Default is 4 (cross). When overlay_mode is "shape", accepts named strings: "cross", "slash", "x".
- overlay_code_affected
Code for affected individuals in overlay. Default is 1.
- overlay_code_unaffected
Code for unaffected individuals in overlay. Default is 0.
- overlay_label_affected
Label for affected individuals in overlay. Default is "Affected".
- overlay_label_unaffected
Label for unaffected individuals in overlay. Default is "Unaffected".
- overlay_alpha_affected
Alpha for affected individuals in overlay. Default is 1.
- overlay_alpha_unaffected
Alpha for unaffected individuals in overlay. Default is 0.
- overlay_color
Color for overlay points. Default is "black".
- overlay_include
Whether to include overlay points in the plot. Default is FALSE.
- overlay_mode
Character string specifying the overlay rendering mode. "alpha" (default) uses alpha transparency mapping; "shape" draws a shape overlay on matching individuals (e.g., cross for deceased markers).
- overlay_size
Numeric. Size of the shape overlay. Default is NULL (inherits from point_size). Only used when overlay_mode is "shape".
- overlay_stroke
Stroke width for the shape overlay. Default is 1.5. Only used when overlay_mode is "shape".
- overlay_legend_title
Title of the overlay legend. Default is "Overlay".
- overlay_legend_show
Whether to show the overlay legend. Default is FALSE.
- focal_fill_include
Whether to fill focal individuals. Default is FALSE.
- focal_fill_legend_show
Whether to show legend for focal fill. Default is TRUE.
- focal_fill_personID
ID of focal individual. Default is 1.
- focal_fill_legend_title
Title of focal fill legend.
- focal_fill_high_color
High-end color for focal gradient.
- focal_fill_mid_color
Midpoint color for focal gradient.
- focal_fill_low_color
Low-end color for focal gradient.
- focal_fill_scale_midpoint
Midpoint for focal fill scale. Default uses color_scale_midpoint.
- focal_fill_method
Method used for focal fill gradient. Options are 'steps', 'steps2', 'step', 'step2', 'viridis_c', 'viridis_d', 'viridis_b', 'manual', 'hue', 'gradient2', 'gradient'.
- focal_fill_component
Component type for focal fill.
- focal_fill_n_breaks
Number of breaks in focal fill scale.
- focal_fill_na_color
Color for NA values in focal fill.
- focal_fill_shape
Shape used for focal fill points.
- focal_fill_force_zero
Whether to force zero to NA in focal fill.
- focal_fill_use_log
Whether to use log scale for focal fill.
- focal_fill_hue_range
Hue range for focal fill colors.
- focal_fill_chroma
Chroma value for focal fill colors.
- focal_fill_lightness
Lightness value for focal fill colors.
- focal_fill_hue_direction
Direction of focal fill gradient.
- focal_fill_viridis_option
Option for viridis color scale.
- focal_fill_viridis_begin
Start of viridis color scale.
- focal_fill_viridis_end
End of viridis color scale.
- focal_fill_viridis_direction
Direction of viridis color scale (1 for left to right, -1 for right to left).
- focal_fill_color_values
A character vector of colors for focal fill.
- focal_fill_labels
Labels for focal fill colors.
- filter_n_pairs
Threshold to filter maximum number of pairs.
- filter_degree_min
Minimum degree value used in filtering.
- filter_degree_max
Maximum degree value used in filtering.
- drop_classic_kin
Whether to exclude classic kin categories.
- drop_non_classic_sibs
Whether to exclude non-classic sibs.
- use_only_classic_kin
Whether to restrict analysis to classic kinship.
- use_relative_degree
Whether to use relative degrees instead of absolute.
- group_by_kin
Whether to group output by kinship group.
- match_threshold_percent
Kinbin matching threshold as a percentage.
- max_degree_levels
Maximum number of degree levels to show.
- grouping_column
Name of column used for grouping.
- annotate_include
Whether to include annotations.
- annotate_x_shift
Horizontal shift applied to annotation text.
- annotate_y_shift
Vertical shift applied to annotation text.
- ci_include
Whether to show confidence intervals.
- ci_ribbon_alpha
Alpha level for CI ribbons.
- tile_color_palette
Color palette for matrix plots. Default is c("white", "gold", "red").
- tile_interpolate
Whether to interpolate colors in matrix tiles.
- tile_color_border
Color border for matrix tiles. Default is NA (no border).
- tile_cluster
Whether to sort by clusters the matrix.
- tile_geom
Geometry type for matrix tiles (e.g., "geom_tile", "geom_raster").
- tile_na_rm
Whether to remove NA values in matrix tiles. Default is FALSE.
- tile_linejoin
Line join type for matrix tiles. Default is "mitre".
- matrix_fill_legend_title
Title for the fill legend in matrix plots. Default is "Relatedness".
- matrix_diagonal_include
Whether to include diagonal in matrix plots. Default is TRUE.
- matrix_upper_triangle_include
Whether to include upper triangle in matrix plots.
- matrix_lower_triangle_include
Whether to include lower triangle in matrix plots.
- matrix_sparse
Whether matrix input is sparse.
- matrix_isChild_method
Method used for isChild matrix derivation. Options are "partialparent", "fullparent", "anyparent".
- return_static
Whether to return a static plot.
- return_widget
Whether to return a widget object.
- return_interactive
Whether to return an interactive plot.
- return_mid_parent
Whether to return mid_parent values in the plot.
- reduce_variables
Whether to reduce the number of variables passed to the plot for performance optimization. Default is TRUE.
- reposition_founders
Whether to reposition founders in the layout. Default is TRUE, which moves founders to the top of the plot and centers them over their descendants. When FALSE, founders are placed according to their original generation assignment, which may be more appropriate for certain types of pedigrees (e.g., those with many generations or non-traditional structures).
- return_best_seed
Whether to return the seed that produced the best layout when `founder_order_tries > 1`. Default is `FALSE`. When `TRUE`, the output includes a `best_seed` attribute with the integer seed that produced the best layout.
- hints
Optional hints to pass along to kinship2::autohint
- relation
Optional relation to pass along to kinship2::pedigree
- debug
Whether to enable debugging mode.
- override_many2many
Whether to override many-to-many link logic.
- optimize_plotly
Whether to optimize the plotly output for speed.
- recode_missing_ids
Whether to recode 0s as missing IDs in the pedigree. Default is TRUE.
- recode_missing_sex
Whether to recode missing sex codes in the pedigree. Default is TRUE.
- add_phantoms
Whether to add phantom parents for individuals without parents.
- affected_fill_include
Whether to enable affected fill styling. Default is FALSE.
- affected_fill_code_affected
Value in the affected fill column that triggers filling. Default is 1.
- affected_fill_code_unaffected
Value in the affected fill column for unaffected individuals. Default is 0.
- affected_fill_label_affected
Label for affected individuals in fill legend. Default is "Affected".
- affected_fill_label_unaffected
Label for unaffected individuals in fill legend. Default is "Unaffected".
- affected_fill_color_affected
Color used to fill symbols for affected individuals. Default is "black".
- affected_fill_color_unaffected
Color used to fill symbols for unaffected individuals. Default is NA (transparent).
- affected_fill_shape_female
Filled shape for affected females. Default is 21 (filled circle).
- affected_fill_shape_male
Filled shape for affected males. Default is 22 (filled square).
- affected_fill_shape_unknown
Filled shape for affected unknown sex. Default is 23 (filled diamond).
- outline_color_include
Whether to enable column-based outline coloring. Default is FALSE.
- outline_color_code_affected
Value in the outline color column that triggers colored outlines. Default is 1.
- outline_color_code_unaffected
Value in the outline color column for default outlines. Default is 0.
- outline_color_label_affected
Label for highlighted outline individuals. Default is "Highlighted".
- outline_color_label_unaffected
Label for default outline individuals. Default is "Default".
- outline_color_affected
Color used for highlighted outlines. Default is "blue".
- outline_color_unaffected
Color used for default (non-highlighted) outlines. Default is "black".
- preset
Optional preset name for default styling combinations. Currently supported: "clinical" for standard clinical pedigree styling. Default is "none" (no preset).
- ...
Additional arguments for future extensibility.