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.
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_palette_default = c("#440154FF", "#FDE725FF", "#21908CFF"),
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,
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,
label_include = TRUE,
label_column = "personID",
label_method = "ggrepel",
label_max_overlaps = 15,
label_nudge_x = 0,
label_nudge_y = -0.1,
label_segment_color = NA,
label_text_angle = 0,
label_text_size = 2,
label_text_color = "black",
label_text_family = "sans",
point_size = 4,
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 = 8,
axis_text_color = "black",
axis_text_family = "sans",
generation_height = 1,
generation_width = 1,
ped_packed = TRUE,
ped_align = TRUE,
ped_width = 15,
segment_linewidth = 0.5,
segment_linetype = 1,
segment_lineend = "round",
segment_linejoin = "round",
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_mz_color = segment_default_color,
segment_mz_linetype = 1,
segment_mz_alpha = 1,
segment_mz_t = 0.6,
segment_self_linetype = "dotdash",
segment_self_linewidth = 0.25,
segment_self_alpha = 0.5,
segment_self_angle = 90,
segment_self_curvature = -0.2,
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,
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_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_value = "black",
focal_fill_shape = 21,
focal_fill_force_zero = 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"),
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_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_midparent = FALSE,
debug = FALSE,
override_many2many = FALSE,
...
)A named list of default plotting and layout parameters.
The name of the function calling this configuration.
The column name for person identifiers in the data.
The column name for affected status in the data.
Default alpha transparency level.
Whether to apply default color scales.
Whether to apply default ggplot2 theme.
A character string for the default color of segments in the plot.
A character vector of default colors for the plot.
Color for the low end of a gradient.
Color for the midpoint of a gradient.
Color for the high end of a gradient.
Midpoint value for continuous color scales.
Name of the color scale used (e.g., "ggthemes::calc").
Default alpha transparency for plot elements.
Main title of the plot.
Subtitle of the plot.
Number of digits to round displayed values.
Integer code for males in data.
Threshold to filter maximum number of pairs.
Minimum degree value used in filtering.
Maximum degree value used in filtering.
Whether to exclude classic kin categories.
Whether to exclude non-classic sibs.
Whether to restrict analysis to classic kinship.
Whether to use relative degrees instead of absolute.
Whether to group output by kinship group.
Kinbin matching threshold as a percentage.
Maximum number of degree levels to show.
Name of column used for grouping.
Whether to include annotations.
Horizontal shift applied to annotation text.
Vertical shift applied to annotation text.
Whether to display labels on plot points.
Column to use for text labels.
Method used for labeling (e.g., ggrepel, geom_text).
Maximum number of overlapping labels.
Horizontal nudge for label text.
Vertical nudge for label text.
Segment color for label connectors.
Text angle for labels.
Font size for labels.
Color of the label text.
Font family for label text.
Size of points drawn in plot.
Whether to include outlines around points.
Multiplier to compute outline size from point size.
Additional size added to outlines.
Alpha transparency for point outlines.
Color used for point outlines.
Whether tooltips are shown in interactive plots.
Columns to include in tooltips.
Label for the X-axis.
Label for the Y-axis.
Angle of X-axis text.
Angle of Y-axis text.
Font size of axis text.
Color of axis text.
Font family for axis text.
Vertical spacing of generations.
Horizontal spacing of generations.
Whether the pedigree should use packed layout.
Whether to align pedigree generations.
Plot width of the pedigree block.
Line width for segments.
Line type for segments.
Line end type for segments.
Line join type for segments.
Color for offspring segments.
Color for parent segments.
Color for self-loop segments.
Color for sibling segments.
Color for spouse segments.
Color for monozygotic twin segments.
Line type for MZ segments.
Alpha for MZ segments.
Tuning parameter for MZ segment layout.
Line type for self-loop segments.
Width of self-loop segment lines.
Alpha value for self-loop segments.
Angle of self-loop segment.
Curvature of self-loop segment.
Whether to color nodes by sex.
Title of the sex legend.
Labels used in sex legend.
A character vector of colors for sex.
Shape for female nodes.
Shape for male nodes.
Shape for unknown sex nodes.
Whether to display affected status.
Value that encodes affected status.
Value that encodes unaffected status.
Label for affected status.
Label for unaffected status.
Alpha for affected individuals.
Alpha for unaffected individuals. Default is 0 (transparent).
A character vector of colors for affected status.
Color for affected individuals.
Color for unaffected individuals.
Shape for affected individuals.
Title of the status legend.
Whether to show the status legend.
Shape used for overlaying points in the plot. Default is 4 (cross).
Code for affected individuals in overlay. Default is 1.
Code for unaffected individuals in overlay. Default is 0.
Label for affected individuals in overlay. Default is "Affected".
Label for unaffected individuals in overlay. Default is "Unaffected".
Alpha for affected individuals in overlay. Default is 1.
Alpha for unaffected individuals in overlay. Default is 0.
Color for overlay points. Default is "black".
Whether to include overlay points in the plot. Default is FALSE.
Title of the overlay legend. Default is "Overlay".
Whether to show the overlay legend. Default is FALSE.
Whether to fill focal individuals.
Whether to show legend for focal fill.
ID of focal individual.
Title of focal fill legend.
High-end color for focal gradient.
Midpoint color for focal gradient.
Low-end color for focal gradient.
Midpoint for focal fill scale.
Method used for focal fill gradient.
Component type for focal fill.
Number of breaks in focal fill scale.
Color for NA values in focal fill.
Shape used for focal fill points.
Whether to force zero to NA in focal fill.
Hue range for focal fill colors.
Chroma value for focal fill colors.
Lightness value for focal fill colors.
Direction of focal fill gradient.
Option for viridis color scale.
Start of viridis color scale.
End of viridis color scale.
Direction of viridis color scale (1 for left to right, -1 for right to left).
A character vector of colors for focal fill.
Labels for focal fill colors.
Whether to show confidence intervals.
Alpha level for CI ribbons.
Color palette for matrix plots.
Whether to interpolate colors in matrix tiles.
Color border for matrix tiles.
Whether to sort by clusters the matrix.
Geometry type for matrix tiles (e.g., "geom_tile", "geom_raster").
Whether to remove NA values in matrix tiles.
Line join type for matrix tiles.
Whether to include diagonal in matrix plots.
Whether to include upper triangle in matrix plots.
Whether to include lower triangle in matrix plots.
Whether matrix input is sparse.
Method used for isChild matrix derivation.
Whether to return a static plot.
Whether to return a widget object.
Whether to return an interactive plot.
Whether to return midparent values in the plot.
Whether to enable debugging mode.
Whether to override many-to-many link logic.
Additional arguments for future extensibility.